Loop the sd values once
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@@ -382,8 +382,6 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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# Use appropriate helper function based on plot type
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plot <- switch(config$plot_type,
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"scatter" = generate_scatter_plot(plot, config),
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"rank" = generate_rank_plot(plot, config),
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"correlation" = generate_correlation_plot(plot, config),
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"box" = generate_box_plot(plot, config),
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"density" = plot + geom_density(),
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"bar" = plot + geom_bar(),
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@@ -439,6 +437,16 @@ generate_scatter_plot <- function(plot, config, interactive = FALSE) {
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}
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}
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# Add SD bands (iterate over sd_band only here)
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if (!is.null(config$sd_band)) {
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for (i in config$sd_band) {
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plot <- plot +
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annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
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annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
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geom_hline(yintercept = c(-i, i), color = "gray")
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}
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}
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# Add error bars if specified
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if (!is.null(config$error_bar) && config$error_bar) {
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y_mean_col <- paste0("mean_", config$y_var)
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@@ -470,42 +478,6 @@ generate_scatter_plot <- function(plot, config, interactive = FALSE) {
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return(plot)
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}
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generate_rank_plot <- function(plot, config) {
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plot <- plot + geom_point(size = config$size %||% 0.1, shape = config$shape %||% 3)
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if (!is.null(config$sd_band)) {
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for (i in seq_len(config$sd_band)) {
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plot <- plot +
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annotate("rect", xmin = -Inf, xmax = Inf, ymin = i, ymax = Inf, fill = "#542788", alpha = 0.3) +
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annotate("rect", xmin = -Inf, xmax = Inf, ymin = -i, ymax = -Inf, fill = "orange", alpha = 0.3) +
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geom_hline(yintercept = c(-i, i), color = "gray")
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}
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}
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if (!is.null(config$enhancer_label)) {
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plot <- plot + annotate("text", x = config$enhancer_label$x, y = config$enhancer_label$y, label = config$enhancer_label$label)
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}
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if (!is.null(config$suppressor_label)) {
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plot <- plot + annotate("text", x = config$suppressor_label$x, y = config$suppressor_label$y, label = config$suppressor_label$label)
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}
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return(plot)
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}
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generate_correlation_plot <- function(plot, config) {
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plot <- plot + geom_point(shape = config$shape %||% 3, color = "gray70") +
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geom_abline(intercept = config$lm_line$intercept, slope = config$lm_line$slope, color = "tomato3") +
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annotate("text", x = config$annotate_position$x, y = config$annotate_position$y, label = config$correlation_text)
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if (!is.null(config$rect)) {
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plot <- plot + geom_rect(aes(xmin = config$rect$xmin, xmax = config$rect$xmax, ymin = config$rect$ymin, ymax = config$rect$ymax),
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color = "grey20", size = 0.25, alpha = 0.1, fill = NA, inherit.aes = FALSE)
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}
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return(plot)
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}
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generate_box_plot <- function(plot, config) {
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plot <- plot + geom_boxplot()
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@@ -524,6 +496,21 @@ generate_box_plot <- function(plot, config) {
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return(plot)
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}
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# Adjust missing values and calculate ranks
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adjust_missing_and_rank <- function(df, variables) {
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# Adjust missing values in Avg_Zscore and Z_lm columns, and apply rank to the specified variables
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df <- df %>%
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mutate(across(all_of(variables), list(
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Avg_Zscore = ~ if_else(is.na(get(paste0("Avg_Zscore_", cur_column()))), 0.001, get(paste0("Avg_Zscore_", cur_column()))),
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Z_lm = ~ if_else(is.na(get(paste0("Z_lm_", cur_column()))), 0.001, get(paste0("Z_lm_", cur_column()))),
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Rank = ~ rank(get(paste0("Avg_Zscore_", cur_column()))),
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Rank_lm = ~ rank(get(paste0("Z_lm_", cur_column())))
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), .names = "{fn}_{col}"))
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return(df)
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}
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generate_interaction_plot_configs <- function(df, variables) {
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configs <- list()
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@@ -632,69 +619,50 @@ generate_interaction_plot_configs <- function(df, variables) {
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return(configs)
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}
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# Adjust missing values and calculate ranks
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adjust_missing_and_rank <- function(df, variables) {
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# Adjust missing values in Avg_Zscore and Z_lm columns, and apply rank to the specified variables
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df <- df %>%
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mutate(across(all_of(variables), list(
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Avg_Zscore = ~ if_else(is.na(get(paste0("Avg_Zscore_", cur_column()))), 0.001, get(paste0("Avg_Zscore_", cur_column()))),
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Z_lm = ~ if_else(is.na(get(paste0("Z_lm_", cur_column()))), 0.001, get(paste0("Z_lm_", cur_column()))),
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Rank = ~ rank(get(paste0("Avg_Zscore_", cur_column()))),
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Rank_lm = ~ rank(get(paste0("Z_lm_", cur_column())))
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), .names = "{fn}_{col}"))
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return(df)
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}
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generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FALSE) {
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configs <- list()
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# Adjust titles for _lm plots if is_lm is TRUE
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plot_title_prefix <- if (is_lm) "Interaction Z score vs. Rank for" else "Average Z score vs. Rank for"
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# Annotated version (with text)
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for (sd_band in c(1, 2, 3)) {
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configs[[length(configs) + 1]] <- list(
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df = df,
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x_var = rank_var,
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y_var = zscore_var,
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plot_type = "rank",
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title = paste(plot_title_prefix, var, "above", sd_band, "SD"),
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sd_band = sd_band,
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enhancer_label = list(
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x = nrow(df) / 2, y = 10,
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label = paste("Deletion Enhancers =", nrow(df[df[[zscore_var]] >= sd_band, ]))
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),
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suppressor_label = list(
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x = nrow(df) / 2, y = -10,
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label = paste("Deletion Suppressors =", nrow(df[df[[zscore_var]] <= -sd_band, ]))
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),
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shape = 3,
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size = 0.1
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)
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}
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# Single config with all sd bands
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configs[[length(configs) + 1]] <- list(
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df = df,
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x_var = rank_var,
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y_var = zscore_var,
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plot_type = "scatter",
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title = paste(plot_title_prefix, var, "Rank Plot"),
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sd_band = c(1, 2, 3), # Pass all sd bands at once
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enhancer_label = list(
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x = nrow(df) / 2, y = 10,
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label = paste("Deletion Enhancers =", nrow(df[df[[zscore_var]] >= 1, ])) # Example for the first SD band
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),
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suppressor_label = list(
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x = nrow(df) / 2, y = -10,
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label = paste("Deletion Suppressors =", nrow(df[df[[zscore_var]] <= -1, ]))
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),
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shape = 3,
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size = 0.1
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)
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# Non-annotated version (_notext)
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for (sd_band in c(1, 2, 3)) {
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configs[[length(configs) + 1]] <- list(
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df = df,
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x_var = rank_var,
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y_var = zscore_var,
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plot_type = "rank",
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title = paste(plot_title_prefix, var, "above", sd_band, "SD"),
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sd_band = sd_band,
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enhancer_label = NULL, # No annotations for _notext
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suppressor_label = NULL, # No annotations for _notext
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shape = 3,
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size = 0.1,
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position = "jitter"
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)
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}
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# Non-annotated version
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configs[[length(configs) + 1]] <- list(
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df = df,
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x_var = rank_var,
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y_var = zscore_var,
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plot_type = "scatter",
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title = paste(plot_title_prefix, var, "Rank Plot No Annotations"),
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sd_band = c(1, 2, 3),
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enhancer_label = NULL,
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suppressor_label = NULL,
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shape = 3,
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size = 0.1,
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position = "jitter"
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)
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return(configs)
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}
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generate_correlation_plot_configs <- function(df, variables) {
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configs <- list()
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@@ -707,7 +675,7 @@ generate_correlation_plot_configs <- function(df, variables) {
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df = df,
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x_var = avg_zscore_var,
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y_var = z_lm_var,
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plot_type = "correlation",
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plot_type = "scatter",
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title = paste("Avg Zscore vs lm", variable),
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color_var = "Overlap",
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correlation_text = paste("R-squared =", round(df[[lm_r_squared_col]][1], 2)),
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