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Add pre-calculated error bars to scatter plots

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Bryan Roessler
2024-09-30 02:21:54 -04:00
parent 039c6c1388
commit 3d11ffbdbc
1 changed files with 61 additions and 56 deletions
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117
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -560,18 +560,30 @@ generate_scatter_plot <- function(plot, config) {
# Add error bars if specified # Add error bars if specified
if (!is.null(config$error_bar) && config$error_bar && !is.null(config$y_var)) { if (!is.null(config$error_bar) && config$error_bar && !is.null(config$y_var)) {
y_mean_col <- paste0("mean_", config$y_var) if (!is.null(config$error_bar_params)) {
y_sd_col <- paste0("sd_", config$y_var) plot <- plot +
geom_errorbar(
plot <- plot + aes(
geom_errorbar( ymin = config$error_bar_params$ymin,
aes( ymax = config$error_bar_params$ymax
ymin = !!sym(y_mean_col) - !!sym(y_sd_col), ),
ymax = !!sym(y_mean_col) + !!sym(y_sd_col) alpha = 0.3,
), linewidth = 0.5
alpha = 0.3, )
linewidth = 0.5 } else {
) y_mean_col <- paste0("mean_", config$y_var)
y_sd_col <- paste0("sd_", config$y_var)
plot <- plot +
geom_errorbar(
aes(
ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
ymax = !!sym(y_mean_col) + !!sym(y_sd_col)
),
alpha = 0.3,
linewidth = 0.5
)
}
} }
# Customize X-axis if specified # Customize X-axis if specified
@@ -675,9 +687,10 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
df_filtered <- df %>% df_filtered <- df %>%
mutate(OrfRepCombined = if (plot_type == "reference") paste(OrfRep, Gene, num, sep = "_") else paste(OrfRep, Gene, sep = "_")) mutate(OrfRepCombined = if (plot_type == "reference") paste(OrfRep, Gene, num, sep = "_") else paste(OrfRep, Gene, sep = "_"))
plots <- list() # Separate the plots into two groups: overall variables and delta comparisons
overall_plots <- list()
delta_plots <- list()
# Generate plots for overall variables (L, K, r, AUC)
for (var in c("L", "K", "r", "AUC")) { for (var in c("L", "K", "r", "AUC")) {
y_limits <- limits_map[[var]] y_limits <- limits_map[[var]]
@@ -692,14 +705,12 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
error_bar = TRUE, error_bar = TRUE,
x_breaks = unique(df_filtered$conc_num_factor_factor), x_breaks = unique(df_filtered$conc_num_factor_factor),
x_labels = as.character(unique(df_filtered$conc_num)), x_labels = as.character(unique(df_filtered$conc_num)),
grid_layout = list(ncol = 2, nrow = 2),
position = "jitter", position = "jitter",
smooth = TRUE smooth = TRUE
) )
plots <- append(plots, list(config)) overall_plots <- append(overall_plots, list(config))
} }
# Generate Delta comparison plots
unique_groups <- df_filtered %>% select(all_of(group_vars)) %>% distinct() unique_groups <- df_filtered %>% select(all_of(group_vars)) %>% distinct()
for (i in seq_len(nrow(unique_groups))) { for (i in seq_len(nrow(unique_groups))) {
@@ -713,13 +724,13 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
for (var in c("Delta_L", "Delta_K", "Delta_r", "Delta_AUC")) { for (var in c("Delta_L", "Delta_K", "Delta_r", "Delta_AUC")) {
y_limits <- limits_map[[var]] y_limits <- limits_map[[var]]
y_span <- y_limits[2] - y_limits[1] y_span <- y_limits[2] - y_limits[1]
# Error bars # Error bars
WT_sd_var <- paste0("WT_sd_", sub("Delta_", "", var)) WT_sd_var <- paste0("WT_sd_", sub("Delta_", "", var))
WT_sd_value <- group_data[[WT_sd_var]][1] WT_sd_value <- group_data[[WT_sd_var]][1]
error_bar_ymin <- 0 - (2 * WT_sd_value) error_bar_ymin <- 0 - (2 * WT_sd_value)
error_bar_ymax <- 0 + (2 * WT_sd_value) error_bar_ymax <- 0 + (2 * WT_sd_value)
# Annotations # Annotations
Z_Shift_value <- round(group_data[[paste0("Z_Shift_", sub("Delta_", "", var))]][1], 2) Z_Shift_value <- round(group_data[[paste0("Z_Shift_", sub("Delta_", "", var))]][1], 2)
Z_lm_value <- round(group_data[[paste0("Z_lm_", sub("Delta_", "", var))]][1], 2) Z_lm_value <- round(group_data[[paste0("Z_lm_", sub("Delta_", "", var))]][1], 2)
@@ -752,14 +763,16 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL, plot_type =
smooth = TRUE, smooth = TRUE,
x_breaks = unique(group_data$conc_num_factor_factor), x_breaks = unique(group_data$conc_num_factor_factor),
x_labels = as.character(unique(group_data$conc_num)), x_labels = as.character(unique(group_data$conc_num)),
ylim_vals = y_limits, ylim_vals = y_limits
grid_layout = list(ncol = 4, nrow = 3)
) )
plots <- append(plots, list(config)) delta_plots <- append(delta_plots, list(config))
} }
} }
return(list(grid_layout = list(ncol = 2, nrow = 2), plots = plots)) return(list(
overall_plots = list(grid_layout = list(ncol = 2, nrow = 2), plots = overall_plots),
delta_plots = list(grid_layout = list(ncol = 4, nrow = 3), plots = delta_plots)
))
} }
generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, adjust = FALSE, overlap_color = FALSE) { generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, adjust = FALSE, overlap_color = FALSE) {
@@ -1046,7 +1059,6 @@ main <- function() {
# Each plots list corresponds to a file # Each plots list corresponds to a file
l_vs_k_plot_configs <- list( l_vs_k_plot_configs <- list(
grid_layout = list(ncol = 1, nrow = 1),
plots = list( plots = list(
list( list(
df = df, df = df,
@@ -1063,7 +1075,6 @@ main <- function() {
) )
frequency_delta_bg_plot_configs <- list( frequency_delta_bg_plot_configs <- list(
grid_layout = list(ncol = 1, nrow = 1),
plots = list( plots = list(
list( list(
df = df_stats, df = df_stats,
@@ -1093,7 +1104,6 @@ main <- function() {
) )
above_threshold_plot_configs <- list( above_threshold_plot_configs <- list(
grid_layout = list(ncol = 1, nrow = 1),
plots = list( plots = list(
list( list(
df = df_above_tolerance, df = df_above_tolerance,
@@ -1145,7 +1155,6 @@ main <- function() {
) )
l_outside_2sd_k_plot_configs <- list( l_outside_2sd_k_plot_configs <- list(
grid_layout = list(ncol = 1, nrow = 1), # Ensures it's compatible with generate_and_save_plots
plots = list( plots = list(
list( list(
df = df_na_l_outside_2sd_k_stats, df = df_na_l_outside_2sd_k_stats,
@@ -1170,7 +1179,6 @@ main <- function() {
) )
delta_bg_outside_2sd_k_plot_configs <- list( delta_bg_outside_2sd_k_plot_configs <- list(
grid_layout = list(ncol = 1, nrow = 1), # Ensures it's compatible with generate_and_save_plots
plots = list( plots = list(
list( list(
df = df_na_l_outside_2sd_k_stats, df = df_na_l_outside_2sd_k_stats,
@@ -1195,37 +1203,34 @@ main <- function() {
) )
message("Generating quality control plots in parallel") message("Generating quality control plots in parallel")
generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plot_configs)
quit()
# # future::plan(future::multicore, workers = parallel::detectCores()) # # future::plan(future::multicore, workers = parallel::detectCores())
# future::plan(future::multisession, workers = 3) # generate 3 plots in parallel future::plan(future::multisession, workers = 3) # generate 3 plots in parallel
# plot_configs <- list( plot_configs <- list(
# list(out_dir = out_dir_qc, filename = "L_vs_K_before_quality_control", 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),
# list(out_dir = out_dir_qc, filename = "frequency_delta_background", list(out_dir = out_dir_qc, filename = "frequency_delta_background",
# plot_configs = frequency_delta_bg_plot_configs), plot_configs = frequency_delta_bg_plot_configs),
# list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold", list(out_dir = out_dir_qc, filename = "L_vs_K_above_threshold",
# plot_configs = above_threshold_plot_configs), plot_configs = above_threshold_plot_configs),
# list(out_dir = out_dir_qc, filename = "plate_analysis", list(out_dir = out_dir_qc, filename = "plate_analysis",
# plot_configs = plate_analysis_plot_configs), plot_configs = plate_analysis_plot_configs),
# list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots", list(out_dir = out_dir_qc, filename = "plate_analysis_boxplots",
# plot_configs = plate_analysis_boxplot_configs), plot_configs = plate_analysis_boxplot_configs),
# list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros", 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),
# list(out_dir = out_dir_qc, filename = "plate_analysis_no_zeros_boxplots", 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),
# list(out_dir = out_dir_qc, filename = "L_vs_K_for_strains_2SD_outside_mean_K", 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),
# list(out_dir = out_dir_qc, filename = "delta_background_vs_K_for_strains_2sd_outside_mean_K", 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)
# ) )
# # Generating quality control plots in parallel # Generating quality control plots in parallel
# furrr::future_map(plot_configs, function(config) { furrr::future_map(plot_configs, function(config) {
# generate_and_save_plots(config$out_dir, config$filename, config$plot_configs) generate_and_save_plots(config$out_dir, config$filename, config$plot_configs)
# }, .options = furrr_options(seed = TRUE)) }, .options = furrr_options(seed = TRUE))
# Process background strains # Process background strains
bg_strains <- c("YDL227C") bg_strains <- c("YDL227C")