updated plotOutliers to include conditional formating for outliers = …

…NULL

R/plotOutliers.R

@@ -13,7 +13,7 @@
 #'   in the plot. This metric should be a column name in `colData(spe)`.
 #' @param outliers A character string specifying the column name in `colData(spe)`
 #'   that indicates whether a data point is considered an outlier. Default is
-#'   "local_outliers".
+#'   NULL.
 #' @param colors A character vector specifying the colors to be used for the
 #'   gradient scale. If length is 2, the gradient will be a single color gradient.
 #' @param stroke A numeric value specifying the border thickness for outlier
@@ -33,33 +33,51 @@
 
 plotOutliers <- function(spe, sample_id = "sample_id",
                         sample=unique(spe$sample_id)[1], metric="detected",
-                        outliers="local_outliers", point_size=1,
+                        outliers=NULL, point_size=1,
                         colors=c("white","black"), stroke=1) {
 
 
+  # Subset the data to the specified sample
   spe.subset <- spe[ ,colData(spe)[[sample_id]] == sample]
 
+  # Start building the plot
   p <- make_escheR(spe.subset) |>
-    add_fill(var = metric, point_size = point_size) |>
-    add_ground(var = outliers, stroke = stroke) +
-    ggtitle(paste0("Sample: ", sample))
+    add_fill(var = metric, point_size = point_size)
 
-  # remove and replace scales (to avoid warnings for re-coloring)
+  # Conditionally add outliers if they are not NULL
+  if (!is.null(outliers)) {
+    p <- p |> add_ground(var = outliers, stroke = stroke)
+  }
+
+  # Add title to the plot
+  p <- p + ggtitle(paste0("Sample: ", sample))
+
+  # Remove and replace scales to avoid warnings for re-coloring
   p$scales$scales <- list()
+
+  # Conditionally add color scales based on the length of 'colors'
   if (length(colors) == 2) {
-    p <- p + scale_fill_gradient(low=colors[1], high=colors[2]) +
-      scale_color_manual(
+    p <- p + scale_fill_gradient(low = colors[1], high = colors[2]) +
+      scale_y_reverse()
+
+    # If outliers are not NULL, add a manual color scale for them
+    if (!is.null(outliers)) {
+      p <- p + scale_color_manual(
         name = "", # turn off legend name for ground
         values = c("TRUE" = "red", "FALSE" = "transparent")
-      ) +
-      scale_y_reverse()
+      )
+    }
   } else if (length(colors) > 2) {
-    p <- p + scale_fill_gradient2(low=colors[1], mid=colors[2], high=colors[3]) +
-      scale_color_manual(
+    p <- p + scale_fill_gradient2(low = colors[1], mid = colors[2], high = colors[3]) +
+      scale_y_reverse()
+
+    # If outliers are not NULL, add a manual color scale for them
+    if (!is.null(outliers)) {
+      p <- p + scale_color_manual(
         name = "", # turn off legend name for ground
         values = c("TRUE" = "red", "FALSE" = "transparent")
-      ) +
-      scale_y_reverse()
+      )
+    }
   }
 
   return(p)