From 19bae34a96b48bb699ce1bc4afda9d8fe2543496 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Mon, 15 Nov 2021 09:21:37 +0100
Subject: [PATCH] plots: Add max_rank to score plot

---
 R/plots.R          | 27 ++++++++++++++++++++++++++-
 man/plot_scores.Rd |  5 ++++-
 2 files changed, 30 insertions(+), 2 deletions(-)

diff --git a/R/plots.R b/R/plots.R
index 6eabcdc..9b2ee0d 100644
--- a/R/plots.R
+++ b/R/plots.R
@@ -7,11 +7,16 @@
 #'   will be highlighted in the plot.
 #' @param labels Labels for the gene sets. This is required if gene sets are
 #'   given and has to have the same length.
+#' @param max_rank The maximum rank of the highlighted genes. All genes that
+#'   are ranked lower will appear greyed out.
 #'
 #' @seealso ranking()
 #'
 #' @export
-plot_scores <- function(ranking, gene_sets = NULL, labels = NULL) {
+plot_scores <- function(ranking,
+                        gene_sets = NULL,
+                        labels = NULL,
+                        max_rank = NULL) {
     if (!requireNamespace("plotly", quietly = TRUE)) {
         stop("Please install \"plotly\" to use this function.")
     }
@@ -60,6 +65,26 @@ plot_scores <- function(ranking, gene_sets = NULL, labels = NULL) {
         )
     }
 
+
+    if (!is.null(max_rank)) {
+        first_not_included_rank <- max_rank + 1
+        last_rank <- ranking[, .N]
+
+        if (first_not_included_rank <= last_rank) {
+            plot <- plot |> plotly::layout(
+                shapes = list(
+                    type = "rect",
+                    fillcolor = "black",
+                    opacity = 0.1,
+                    x0 = first_not_included_rank,
+                    x1 = last_rank,
+                    y0 = 0.0,
+                    y1 = 1.0
+                )
+            )
+        }
+    }
+
     plot
 }
 
diff --git a/man/plot_scores.Rd b/man/plot_scores.Rd
index a09c590..78d01e8 100644
--- a/man/plot_scores.Rd
+++ b/man/plot_scores.Rd
@@ -4,7 +4,7 @@
 \alias{plot_scores}
 \title{Plot a ranking as a scatter plot of scores.}
 \usage{
-plot_scores(ranking, gene_sets = NULL, labels = NULL)
+plot_scores(ranking, gene_sets = NULL, labels = NULL, max_rank = NULL)
 }
 \arguments{
 \item{ranking}{The ranking to visualize.}
@@ -14,6 +14,9 @@ will be highlighted in the plot.}
 
 \item{labels}{Labels for the gene sets. This is required if gene sets are
 given and has to have the same length.}
+
+\item{max_rank}{The maximum rank of the highlighted genes. All genes that
+are ranked lower will appear greyed out.}
 }
 \description{
 This function requires the package \code{plotly}.