Generalize generate_and_save_plots() further
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@@ -306,6 +306,7 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
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Z_lm_AUC = (lm_Score_AUC - mean(lm_Score_AUC, na.rm = TRUE)) / sd(lm_Score_AUC, na.rm = TRUE)
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)
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# Declare column order for output
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calculations <- calculations %>%
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select("OrfRep", "Gene", "num", "conc_num", "conc_num_factor",
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"mean_L", "mean_K", "mean_r", "mean_AUC",
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@@ -320,7 +321,7 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
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"NG", "SM", "DB") %>%
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ungroup()
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# Arrange results by Z_lm_L and NG
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# Also arrange results by Z_lm_L and NG
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interactions <- interactions %>%
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select("OrfRep", "Gene", "num", "Raw_Shift_L", "Raw_Shift_K", "Raw_Shift_AUC", "Raw_Shift_r",
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"Z_Shift_L", "Z_Shift_K", "Z_Shift_r", "Z_Shift_AUC",
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@@ -339,23 +340,41 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
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generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) {
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message("Generating html and pdf plots for: ", file_name)
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message("Generating html and pdf plots for: ", file_name, ".pdf|html")
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plots <- lapply(plot_configs, function(config) {
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# Log configuration details
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message("title: ", config$title)
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message("plot_type: ", config$plot_type)
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message("x_var: ", config$x_var)
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message("y_var: ", config$y_var)
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message("error_bar: ", config$error_bar)
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df <- config$df
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# Check if y_var is NULL and adjust the aes mapping
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# Build the aes mapping depending on whether y_var is present
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aes_mapping <- if (is.null(config$y_var)) {
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aes(x = !!sym(config$x_var), color = as.factor(!!sym(config$color_var)))
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} else {
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aes(x = !!sym(config$x_var), y = !!sym(config$y_var), color = as.factor(!!sym(config$color_var)))
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}
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# Initialize the plot with ggplot
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plot <- ggplot(df, aes_mapping)
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# Handle plot types like "rank", "correlation", and default scatter/box/density
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if (config$plot_type == "rank") {
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# Handle plot types explicitly
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if (config$plot_type == "scatter") {
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plot <- plot + geom_point(shape = 3)
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# Add geom_smooth only if specified
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if (!is.null(config$add_smooth) && config$add_smooth) {
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plot <- plot + geom_smooth(method = "lm", se = FALSE)
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}
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} else if (config$plot_type == "rank") {
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plot <- plot + geom_point(size = 0.1, shape = 3)
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if (!is.null(config$sd_band)) {
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for (i in seq_len(config$sd_band)) {
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plot <- plot +
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@@ -364,17 +383,16 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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geom_hline(yintercept = c(-i, i), color = "gray")
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}
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}
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if (!is.null(config$enhancer_label)) {
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plot <- plot + annotate("text", x = config$enhancer_label$x, y = config$enhancer_label$y,
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label = config$enhancer_label$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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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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} else if (config$plot_type == "correlation") {
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plot <- plot + geom_point(shape = 3, color = "gray70") + geom_smooth(method = "lm", color = "tomato3") +
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plot <- plot + geom_point(shape = 3, color = "gray70") +
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geom_smooth(method = "lm", color = "tomato3") +
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annotate("text", x = 0, y = 0, label = config$correlation_text)
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} else {
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# Adjust based on plot types that may or may not need y_var
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if (config$plot_type == "box") {
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} else if (config$plot_type == "box") {
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plot <- plot + geom_boxplot()
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} else if (config$plot_type == "density") {
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plot <- plot + geom_density()
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@@ -383,13 +401,13 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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} else {
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plot <- plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)
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}
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}
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# Add error bars for "delta_bg" or general cases
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# Handle error bars if needed
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if (!is.null(config$error_bar) && config$error_bar) {
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y_mean_col <- paste0("mean_", config$y_var)
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y_sd_col <- paste0("sd_", config$y_var)
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plot <- plot + geom_errorbar(aes(ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
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plot <- plot + geom_errorbar(aes(
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ymin = !!sym(y_mean_col) - !!sym(y_sd_col),
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ymax = !!sym(y_mean_col) + !!sym(y_sd_col)), width = 0.1) +
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geom_point(aes(y = !!sym(y_mean_col)), size = 0.6)
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}
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@@ -399,27 +417,30 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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plot <- plot + coord_cartesian(ylim = config$ylim_vals)
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}
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# Apply labels, titles, and legends
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# Apply titles, labels, and legends
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plot <- plot + ggtitle(config$title) +
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theme_publication(legend_position = if (!is.null(config$legend_position)) config$legend_position else "bottom") +
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xlab(config$x_label %||% "") + ylab(config$y_label %||% "")
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# Add annotations if available
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# Add any annotations
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if (!is.null(config$annotations)) {
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plot <- plot + geom_text(aes(x = config$annotations$x, y = config$annotations$y, label = config$annotations$label))
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for (annotation in config$annotations) {
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plot <- plot + geom_text(aes(x = annotation$x, y = annotation$y, label = annotation$label))
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}
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}
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return(plot)
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})
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# Save the plots
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# Save the plots as PDF
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pdf(file.path(output_dir, paste0(file_name, ".pdf")), width = 14, height = 9)
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lapply(plots, print)
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dev.off()
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# Convert ggplot to plotly for interactive HTML output
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plotly_plots <- lapply(plots, function(plot) suppressWarnings(ggplotly(plot) %>% layout(legend = list(orientation = "h"))))
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# Handle grid layout
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# Combine plots in grid layout if applicable
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combined_plot <- subplot(plotly_plots, nrows = if (!is.null(grid_layout)) grid_layout$nrow else length(plots), margin = 0.05)
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saveWidget(combined_plot, file = file.path(output_dir, paste0(file_name, ".html")), selfcontained = TRUE)
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}
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@@ -996,7 +1017,7 @@ main <- function() {
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group_by(across(all_of(group_vars))) %>%
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filter(!is.na(Z_lm_L) | !is.na(Avg_Zscore_L))
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# Final filtered correaltion calculations and plots
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# Final filtered correlation calculations and plots
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zscores_interactions_filtered <- zscores_interactions_filtered %>%
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mutate(
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Overlap = case_when(
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