Make grid lines configurable

qhtcp-workflow/apps/r/calculate_interaction_zscores.R

@@ -685,6 +685,22 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
       if (!is.null(config$y_label)) plot <- plot + ylab(config$y_label)
       if (!is.null(config$coord_cartesian)) plot <- plot + coord_cartesian(ylim = config$coord_cartesian)
 
+      if (!is.null(config$axis_text_size)) {
+        plot <- plot + theme(
+          axis.text.x = element_text(size = config$axis_text_size$x),
+          axis.text.y = element_text(size = config$axis_text_size$y),
+          axis.title.x = element_text(size = config$axis_title_size$x),
+          axis.title.y = element_text(size = config$axis_title_size$y)
+        )
+      }
+
+      if (!is.null(config$grid_lines)) {
+        plot <- plot + theme(
+          panel.grid.major = if (config$grid_lines$major) element_line() else element_blank(),
+          panel.grid.minor = if (config$grid_lines$minor) element_line() else element_blank()
+        )
+      }
+
       #plotly_plot <- suppressWarnings(plotly::ggplotly(plot))
 
       static_plots[[i]] <- plot
@@ -736,8 +752,6 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
 generate_scatter_plot <- function(plot, config) {
 
   # Define the points
-  shape <- if (!is.null(config$shape)) config$shape else 3
-  size <- if (!is.null(config$size)) config$size else 1.5
   position <-
     if (!is.null(config$position) && config$position == "jitter") {
       position_jitter(width = 0.4, height = 0.1)
@@ -746,8 +760,9 @@ generate_scatter_plot <- function(plot, config) {
     }
 
   plot <- plot + geom_point(
-    shape = shape,
+    shape = ifelse(!is.null(config$shape), config$shape, 3),
-    size = size,
+    size = ifelse(!is.null(config$size), config$size, 1.5),
+    color = ifelse(!is.null(config$color), config$color, "black"),
     position = position
   )
 
@@ -900,22 +915,6 @@ generate_scatter_plot <- function(plot, config) {
       )
   }
 
-  # # Add rectangles if specified
-  # if (!is.null(config$rectangles)) {
-  #   for (rect in config$rectangles) {
-  #     plot <- plot + annotate(
-  #       "rect",
-  #       xmin = rect$xmin,
-  #       xmax = rect$xmax,
-  #       ymin = rect$ymin,
-  #       ymax = rect$ymax,
-  #       fill = ifelse(is.null(rect$fill), NA, rect$fill),
-  #       color = ifelse(is.null(rect$color), "black", rect$color),
-  #       alpha = ifelse(is.null(rect$alpha), 0.1, rect$alpha)
-  #     )
-  #   }
-  # }
-
   # Customize X-axis if specified
   if (!is.null(config$x_breaks) && !is.null(config$x_labels) && !is.null(config$x_label)) {
     # Check if x_var is factor or character (for discrete x-axis)
@@ -1283,7 +1282,7 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, filter_na = FALSE, ove
 generate_correlation_plot_configs <- function(df, df_reference) {
   # Define relationships for different-variable correlations
   relationships <- list(
-    list(x = "L", y = "K"), # x-var is predictor, y-var is reponse
+    list(x = "L", y = "K"),
     list(x = "L", y = "r"),
     list(x = "L", y = "AUC"),
     list(x = "K", y = "r"),
@@ -1304,61 +1303,55 @@ generate_correlation_plot_configs <- function(df, df_reference) {
 
   for (highlight_cyan in highlight_cyan_options) {
     for (rel in relationships) {
-      # Extract relevant variable names for Z_lm values
+      x_var <- paste0("Z_lm_", rel$x)
-      x_var <- paste0("Z_lm_", rel$x) # predictor
+      y_var <- paste0("Z_lm_", rel$y)
-      y_var <- paste0("Z_lm_", rel$y) # response
+      
-
-      print(paste("rel$x:", rel$x))
-      print(paste("rel$y:", rel$y))
-      print(paste("Generating correlation plot for response(y):", y_var, "and predictor(x):", x_var))
-      print(paste("Relationship suffix:", rel$y, "_", rel$x))
-
-      # Extract the R-squared, intercept, and slope from the df (first value)
       intercept <- df[[paste0("Z_lm_intercept_", rel$y, "_", rel$x)]][1]
       slope <- df[[paste0("Z_lm_slope_", rel$y, "_", rel$x)]][1]
       r_squared <- df[[paste0("Z_lm_R_squared_", rel$y, "_", rel$x)]][1]
-
-      print(paste("intercept:", intercept))
-      print(paste("slope:", slope))
-      print(paste("r_squared:", r_squared))
-
       r_squared_rounded <- round(r_squared, 4)
       r_squared_label <- paste("R-squared =", r_squared_rounded)
-      print(paste("r_squared_label:", r_squared_label))
 
-      # Find the max and min of both dataframes for printing linear regression line
       xmin <- min(c(min(df[[x_var]]), min(df_reference[[x_var]])))
       xmax <- max(c(max(df[[x_var]]), max(df_reference[[x_var]])))
 
-      # Generate the label for the plot
+      plot_label <- paste("Interaction", rel$x, "vs. Interaction", rel$y)
-      plot_label <- paste("Interaction", rel$x, "vs.", rel$y)
 
-      # Construct plot config
+      if (highlight_cyan) {
-      plot_config <- list(
+        lm_line <- NULL
-        df = df,
+      } else {
-        df_reference = df_reference,
+        lm_line <- list(
-        x_var = x_var,
-        y_var = y_var,
-        plot_type = "scatter",
-        title = plot_label,
-        annotations = list(
-          list(
-            x = mean(df[[x_var]], na.rm = TRUE),
-            y = mean(df[[y_var]], na.rm = TRUE),
-            label = r_squared_label
-          )
-        ),
-        lm_line = list(
           intercept = intercept,
           slope = slope,
           color = "tomato3",
           linewidth = 0.8,
           xmin = xmin,
           xmax = xmax
-        ),
+        )
+      }
+
+      plot_config <- list(
+        df = df,
+        df_reference = df_reference,
+        x_var = x_var,
+        y_var = y_var,
+        x_label = paste("z-score", rel$x),
+        y_label = paste("z-score", rel$y),
+        plot_type = "scatter",
+        title = plot_label,
         color = "gray70",
-        filter_na = TRUE,
+        annotations = list(
-        cyan_points = highlight_cyan # include cyan points or not based on the loop
+          list(
+            x = mean(df[[x_var]]),
+            y = mean(df[[y_var]]),
+            label = r_squared_label
+          )
+        ),
+        lm_line = lm_line,
+        cyan_points = highlight_cyan,
+        axis_text_size = list(x = 16, y = 16),
+        axis_title_size = list(x = 18, y = 18),
+        grid_lines = list(major = FALSE, minor = FALSE)
       )
 
       plot_configs <- append(plot_configs, list(plot_config))
@@ -1804,7 +1797,27 @@ main <- function() {
       )
       generate_and_save_plots(out_dir, "correlation_cpps", correlation_plot_configs,
         page_width = 10, page_height = 7)
+
+      # TODO for now quit after one iteration
+      quit()
     })
   })
 }
 main()
+
+# For generate_scatter_plot()
+# # Add rectangles if specified
+# if (!is.null(config$rectangles)) {
+#   for (rect in config$rectangles) {
+#     plot <- plot + annotate(
+#       "rect",
+#       xmin = rect$xmin,
+#       xmax = rect$xmax,
+#       ymin = rect$ymin,
+#       ymax = rect$ymax,
+#       fill = ifelse(is.null(rect$fill), NA, rect$fill),
+#       color = ifelse(is.null(rect$color), "black", rect$color),
+#       alpha = ifelse(is.null(rect$alpha), 0.1, rect$alpha)
+#     )
+#   }
+# }

qhtcp-workflow/qhtcp-workflow

@@ -1497,6 +1497,9 @@ calculate_interaction_zscores() {
     "${@:4}" \
     "${EXP_PATHS_AND_NAMES_AND_SD_FACTORS[@]}"
 
+  # TODO for teting exit here so we don't move onto EXP2 accidentally
+  exit $?
+
 }