Add more aes to generate_and_save_plots()
This commit is contained in:
@@ -344,65 +344,66 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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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$error_bar)
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# Log details and setup
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df <- config$df
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aes_mapping <-
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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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# 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 explicitly
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if (config$plot_type == "scatter") {
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plot <- plot + geom_point(shape = 3)
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# Plot type handling
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plot <- switch(config$plot_type,
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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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"scatter" = {
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plot + geom_point(aes(ORF = ORF, Gene = Gene, !!sym(config$x_var) := !!sym(config$x_var)),
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shape = config$shape %||% 3, size = config$size %||% 0.6) +
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(if (!is.null(config$add_smooth) && config$add_smooth)
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geom_smooth(method = "lm", se = FALSE)
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else NULL) +
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(if (!is.null(config$position) && config$position == "jitter")
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geom_point(position = "jitter")
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else NULL) +
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# Use precalculated mean and sd for error bars
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geom_errorbar(aes(
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ymin = !!sym(paste0("mean_", config$y_var)) - !!sym(paste0("sd_", config$y_var)),
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ymax = !!sym(paste0("mean_", config$y_var)) + !!sym(paste0("sd_", config$y_var))), width = 0.1) +
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geom_point(aes(y = !!sym(paste0("mean_", config$y_var))), size = 0.6)
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},
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} else if (config$plot_type == "rank") {
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plot <- plot + geom_point(size = 0.1, shape = 3)
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"rank" = {
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plot + geom_point(size = config$size %||% 0.1, shape = config$shape %||% 3) +
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(if (!is.null(config$sd_band))
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Reduce(`+`, lapply(seq_len(config$sd_band), function(i) {
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list(
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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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})) else NULL) +
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(if (!is.null(config$enhancer_label))
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annotate("text", x = config$enhancer_label$x, y = config$enhancer_label$y, label = config$enhancer_label$label)
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else NULL) +
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(if (!is.null(config$suppressor_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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else NULL)
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},
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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$label) +
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annotate("text", x = config$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") +
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"correlation" = plot + geom_point(shape = config$shape %||% 3, color = "gray70") +
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geom_smooth(method = "lm", color = "tomato3") +
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annotate("text", x = 0, y = 0, label = config$correlation_text)
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} else 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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} else if (config$plot_type == "bar") {
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plot <- plot + geom_bar()
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} else {
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plot <- plot + geom_point(shape = 3) + geom_smooth(method = "lm", se = FALSE)
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}
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annotate("text", x = 0, y = 0, label = config$correlation_text),
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# Handle error bars if needed
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"box" = plot + geom_boxplot(),
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"density" = plot + geom_density(),
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"bar" = plot + geom_bar(),
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# Default case (scatter with smooth line)
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plot + geom_point(shape = config$shape %||% 3) + geom_smooth(method = "lm", se = FALSE)
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)
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# Error bars using pre-calculated mean and sd columns
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if (!is.null(config$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$y_var)
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@@ -412,17 +413,13 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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geom_point(aes(y = !!sym(y_mean_col)), size = 0.6)
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}
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# Apply y-limits if provided
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if (!is.null(config$ylim_vals)) {
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plot <- plot + coord_cartesian(ylim = config$ylim_vals)
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}
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# Apply titles, labels, and legends
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plot <- plot + ggtitle(config$title) +
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theme_publication(legend_position = if (!is.null(config$legend_position)) config$legend_position else "bottom") +
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# Y-limits and labels
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plot <- plot + (if (!is.null(config$ylim_vals)) coord_cartesian(ylim = config$ylim_vals) else NULL) +
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ggtitle(config$title) +
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theme_publication(legend_position = config$legend_position %||% "bottom") +
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xlab(config$x_label %||% "") + ylab(config$y_label %||% "")
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# Add any annotations
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# Annotations
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if (!is.null(config$annotations)) {
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for (annotation in config$annotations) {
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plot <- plot + geom_text(aes(x = annotation$x, y = annotation$y, label = annotation$label))
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@@ -432,16 +429,13 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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return(plot)
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})
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# Save the plots as PDF
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# Save plots to PDF and HTML
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pdf(file.path(output_dir, paste0(file_name, ".pdf")), width = 14, height = 9)
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lapply(plots, print)
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dev.off()
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# Convert ggplot to plotly for interactive HTML output
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plotly_plots <- lapply(plots, function(plot) suppressWarnings(ggplotly(plot) %>% layout(legend = list(orientation = "h"))))
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# Combine plots in grid layout if applicable
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combined_plot <- subplot(plotly_plots, nrows = if (!is.null(grid_layout)) grid_layout$nrow else length(plots), margin = 0.05)
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combined_plot <- subplot(plotly_plots, nrows = grid_layout$nrow %||% length(plots), margin = 0.05)
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saveWidget(combined_plot, file = file.path(output_dir, paste0(file_name, ".html")), selfcontained = TRUE)
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}
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@@ -492,7 +486,10 @@ generate_interaction_plot_configs <- function(df, variables) {
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),
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x_breaks = unique(df$conc_num_factor),
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x_labels = unique(as.character(df$conc_num)),
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x_label = unique(df$Drug[1])
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x_label = unique(df$Drug[1]),
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shape = 3,
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size = 0.6,
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position = "jitter"
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)
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# Add box plot configuration for this variable
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@@ -551,10 +548,11 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA
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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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),
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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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# Non-annotated version (_notext)
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@@ -567,7 +565,10 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA
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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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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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@@ -590,6 +591,8 @@ generate_correlation_plot_configs <- function(df, variables) {
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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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shape = 3,
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geom_smooth = TRUE,
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legend_position = "right"
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)
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}
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@@ -626,7 +629,7 @@ main <- function() {
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# Remove rows with 0 values in L
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df_no_zeros <- df_na %>% filter(L > 0)
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# Set some constants
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# Save some constants
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max_conc <- max(df$conc_num_factor)
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l_half_median <- (median(df_above_tolerance$L, na.rm = TRUE)) / 2
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k_half_median <- (median(df_above_tolerance$K, na.rm = TRUE)) / 2
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@@ -705,46 +708,56 @@ main <- function() {
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plot_type = "scatter",
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title = "Raw L vs K before quality control",
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color_var = "conc_num",
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position = "jitter",
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legend_position = "right"
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)
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)
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frequency_delta_bg_plots <- list(
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list(
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df = df_filtered_stats,
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x_var = "delta_bg",
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y_var = NULL,
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plot_type = "density",
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title = "Plate analysis by Drug Conc for Delta Background before quality control",
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color_var = "conc_num",
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x_label = "Delta Background",
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y_label = "Density",
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error_bar = FALSE,
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legend_position = "right"),
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list(
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df = df_filtered_stats,
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x_var = "delta_bg",
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y_var = NULL,
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plot_type = "bar",
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title = "Plate analysis by Drug Conc for Delta Background before quality control",
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color_var = "conc_num",
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x_label = "Delta Background",
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y_label = "Count",
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error_bar = FALSE,
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legend_position = "right")
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)
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above_threshold_plots <- list(
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list(
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df = df_above_tolerance,
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x_var = "L",
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y_var = "K",
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plot_type = "scatter",
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title = paste("Raw L vs K for strains above delta background threshold of",
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title = paste("Raw L vs K for strains above Delta Background threshold of",
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df_above_tolerance$delta_bg_tolerance[[1]], "or above"),
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color_var = "conc_num",
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position = "jitter",
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annotations = list(
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x = l_half_median,
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y = k_half_median,
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label = paste("Strains above delta background tolerance =", nrow(df_above_tolerance))
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label = paste("# strains above Delta Background tolerance =", nrow(df_above_tolerance))
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),
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error_bar = FALSE,
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legend_position = "right"
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)
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)
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frequency_delta_bg_plots <- list(
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list(df = df_filtered_stats, x_var = "delta_bg", y_var = NULL, plot_type = "density",
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title = "Plate analysis by Drug Conc for delta background before quality control",
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color_var = "conc_num",
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x_label = "Delta Background",
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y_label = "Density",
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error_bar = FALSE,
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legend_position = "right"),
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list(df = df_filtered_stats, x_var = "delta_bg", y_var = NULL, plot_type = "bar",
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title = "Plate analysis by Drug Conc for delta background before quality control",
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color_var = "conc_num",
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x_label = "Delta Background",
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y_label = "Count",
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error_bar = FALSE,
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legend_position = "right")
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)
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plate_analysis_plots <- list()
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for (var in summary_vars) {
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for (stage in c("before", "after")) {
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@@ -760,7 +773,9 @@ main <- function() {
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y_var = var,
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plot_type = "scatter",
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title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
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error_bar = TRUE, color_var = "conc_num")
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error_bar = TRUE,
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color_var = "conc_num",
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position = "jitter")
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plate_analysis_plots <- append(plate_analysis_plots, list(config))
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}
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@@ -797,7 +812,8 @@ main <- function() {
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plot_type = "scatter",
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title = paste("Plate analysis by Drug Conc for", var, "after quality control"),
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error_bar = TRUE,
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color_var = "conc_num")
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color_var = "conc_num",
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position = "jitter")
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plate_analysis_no_zeros_plots <- append(plate_analysis_no_zeros_plots, list(config))
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}
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@@ -827,6 +843,7 @@ main <- function() {
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plot_type = "scatter",
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title = "Raw L vs K for strains falling outside 2SD of the K mean at each Conc",
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color_var = "conc_num",
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position = "jitter",
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legend_position = "right"
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)
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)
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@@ -839,14 +856,15 @@ main <- function() {
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plot_type = "scatter",
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title = "Delta Background vs K for strains falling outside 2SD of the K mean at each Conc",
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color_var = "conc_num",
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position = "jitter",
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legend_position = "right"
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)
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)
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message("Generating QC plots")
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generate_and_save_plots(out_dir_qc, "L_vs_K_before_quality_control", l_vs_k_plots)
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generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots)
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generate_and_save_plots(out_dir_qc, "frequency_delta_background", frequency_delta_bg_plots)
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generate_and_save_plots(out_dir_qc, "L_vs_K_above_threshold", above_threshold_plots)
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generate_and_save_plots(out_dir_qc, "plate_analysis", plate_analysis_plots)
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generate_and_save_plots(out_dir_qc, "plate_analysis_boxplots", plate_analysis_boxplots)
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generate_and_save_plots(out_dir_qc, "plate_analysis_no_zeros", plate_analysis_no_zeros_plots)
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