Add cross-interaction linear model calculations
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@@ -458,49 +458,78 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
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generate_scatter_plot <- function(plot, config) {
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if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
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plot <- plot + geom_point(
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shape = config$shape %||% 3,
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size = config$size %||% 0.2
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)
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} else if (!is.null(config$gene_point) && config$gene_point) {
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plot <- plot + geom_point(
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shape = config$shape %||% 3,
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size = config$size %||% 0.2,
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position = "jitter"
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)
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# 1. Determine Shape, Size, and Position for geom_point
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shape <- if (!is.null(config$shape)) config$shape else 3
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size <- if (!is.null(config$size)) {
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config$size
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} else {
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plot <- plot + geom_point(
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shape = config$shape %||% 3,
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position = if (!is.null(config$position) && config$position == "jitter") "jitter" else "identity",
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size = config$size %||% 0.1
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)
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if (!is.null(config$delta_bg_point) && config$delta_bg_point) 0.2
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else if (!is.null(config$gene_point) && config$gene_point) 0.2
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else 0.1
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}
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# Add smooth line if specified
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position <- if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
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"identity"
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} else if (!is.null(config$gene_point) && config$gene_point) {
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"jitter"
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} else {
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if (!is.null(config$position) && config$position == "jitter") "jitter" else "identity"
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}
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# 2. Add geom_point with determined parameters
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plot <- plot + geom_point(shape = shape, size = size, position = position)
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# 3. Add Smooth Line if specified
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if (!is.null(config$add_smooth) && config$add_smooth) {
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if (!is.null(config$lm_line)) {
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plot <- plot + geom_abline(intercept = config$lm_line$intercept, slope = config$lm_line$slope, color = "blue")
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plot <- plot +
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geom_abline(
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intercept = config$lm_line$intercept,
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slope = config$lm_line$slope,
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color = "blue"
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)
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} else {
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plot <- plot + geom_smooth(method = "lm", se = FALSE, color = "blue")
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plot <- plot +
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geom_smooth(
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method = "lm",
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se = FALSE,
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color = "blue"
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)
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}
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}
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# Add SD bands if specified
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# 4. Add SD Bands if specified
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if (!is.null(config$sd_band_values)) {
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for (sd_band in config$sd_band_values) {
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plot <- plot +
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annotate("rect", xmin = -Inf, xmax = Inf, ymin = sd_band, ymax = Inf, fill = "#542788", alpha = 0.3) +
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annotate("rect", xmin = -Inf, xmax = Inf, ymin = -sd_band, ymax = -Inf, fill = "orange", alpha = 0.3) +
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geom_hline(yintercept = c(-sd_band, sd_band), color = "gray")
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annotate(
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"rect",
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xmin = -Inf, xmax = Inf,
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ymin = sd_band, ymax = Inf,
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fill = "#542788",
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alpha = 0.3
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) +
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annotate(
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"rect",
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xmin = -Inf, xmax = Inf,
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ymin = -sd_band, ymax = -Inf,
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fill = "orange",
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alpha = 0.3
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) +
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geom_hline(
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yintercept = c(-sd_band, sd_band),
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color = "gray"
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)
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}
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}
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# Add error bars if specified
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# 5. 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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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(
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plot <- plot +
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geom_errorbar(
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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)
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@@ -509,29 +538,32 @@ generate_scatter_plot <- function(plot, config) {
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)
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}
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# Add x-axis customization if specified
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# 6. Customize X-axis if specified
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if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
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plot <- plot + scale_x_discrete(
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plot <- plot +
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scale_x_discrete(
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name = config$x_label,
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breaks = config$x_breaks,
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labels = config$x_labels
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)
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}
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# Use coord_cartesian for zooming in without removing data outside the range
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# 7. Apply coord_cartesian if specified
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if (!is.null(config$coord_cartesian)) {
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plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
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}
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# Use scale_y_continuous for setting the y-axis limits
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# 8. Set Y-axis limits if specified
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if (!is.null(config$ylim_vals)) {
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plot <- plot + scale_y_continuous(limits = config$ylim_vals)
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}
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# Add annotations if specified
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# 9. Add Annotations if specified
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if (!is.null(config$annotations)) {
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for (annotation in config$annotations) {
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plot <- plot + annotate("text",
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plot <- plot +
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annotate(
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"text",
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x = annotation$x,
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y = annotation$y,
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label = annotation$label,
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@@ -540,11 +572,12 @@ generate_scatter_plot <- function(plot, config) {
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}
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}
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# Add titles and themes if specified
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# 10. Add Title if specified
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if (!is.null(config$title)) {
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plot <- plot + ggtitle(config$title)
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}
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# 11. Adjust Legend Position if specified
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if (!is.null(config$legend_position)) {
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plot <- plot + theme(legend.position = config$legend_position)
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}
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@@ -552,7 +585,6 @@ generate_scatter_plot <- function(plot, config) {
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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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@@ -794,30 +826,41 @@ generate_rank_plot_configs <- function(df_filtered, is_lm = FALSE, adjust = FALS
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}
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generate_correlation_plot_configs <- function(df) {
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# Define relationships for plotting
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relationships <- list(
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list(x = "Z_lm_L", y = "Z_lm_K", label = "Interaction L vs. Interaction K"),
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list(x = "Z_lm_L", y = "Z_lm_r", label = "Interaction L vs. Interaction r"),
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list(x = "Z_lm_L", y = "Z_lm_AUC", label = "Interaction L vs. Interaction AUC"),
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list(x = "Z_lm_K", y = "Z_lm_r", label = "Interaction K vs. Interaction r"),
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list(x = "Z_lm_K", y = "Z_lm_AUC", label = "Interaction K vs. Interaction AUC"),
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list(x = "Z_lm_r", y = "Z_lm_AUC", label = "Interaction r vs. Interaction AUC")
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)
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configs <- list()
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variables <- c("r", "L", "K", "AUC")
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for (rel in relationships) {
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# Fit linear model
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lm_model <- lm(as.formula(paste(rel$y, "~", rel$x)), data = df)
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lm_summary <- summary(lm_model)
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for (variable in variables) {
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z_lm_var <- paste0("Z_lm_", variable)
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avg_zscore_var <- paste0("Avg_Zscore_", variable)
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lm_r_squared_col <- paste0("lm_R_squared_", variable)
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configs[[length(configs) + 1]] <- list(
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# Construct plot configuration
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config <- list(
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df = df,
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x_var = avg_zscore_var,
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y_var = z_lm_var,
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x_var = rel$x,
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y_var = rel$y,
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plot_type = "scatter",
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title = paste("Avg Zscore vs lm", variable),
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color_var = "Overlap",
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correlation_text = paste("R-squared =", round(df[[lm_r_squared_col]][1], 2)),
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shape = 3,
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geom_smooth = TRUE,
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rect = list(xmin = -2, xmax = 2, ymin = -2, ymax = 2), # To add the geom_rect layer
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annotate_position = list(x = 0, y = 0), # Position for the R-squared text
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title = rel$label,
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x_label = paste("z-score", gsub("Z_lm_", "", rel$x)),
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y_label = paste("z-score", gsub("Z_lm_", "", rel$y)),
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annotations = list(
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list(x = 0, y = 0, label = paste("R-squared =", round(lm_summary$r.squared, 3)))
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),
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add_smooth = TRUE, # This flags that a geom_smooth layer should be added
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lm_line = list(intercept = coef(lm_model)[1], slope = coef(lm_model)[2]), # For direct geom_abline if needed
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legend_position = "right"
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)
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configs[[length(configs) + 1]] <- config
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}
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return(configs)
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