From d075380559d9d2d039bddeefe38e581540701099 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Fri, 5 Nov 2021 23:05:40 +0100
Subject: [PATCH] ranking: Add plot method

---
 DESCRIPTION                 |  1 +
 NAMESPACE                   |  1 +
 R/ranking.R                 | 56 +++++++++++++++++++++++++++++++++++++
 man/plot.geposan_ranking.Rd | 20 +++++++++++++
 4 files changed, 78 insertions(+)
 create mode 100644 man/plot.geposan_ranking.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 4738307..a74b1fe 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,6 +26,7 @@ Imports:
     rlang
 Suggests:
     biomaRt,
+    plotly,
     rlog,
     stringr,
     usethis
diff --git a/NAMESPACE b/NAMESPACE
index 4d93e2b..4a4b515 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(plot,geposan_ranking)
 S3method(print,geposan_comparison)
 S3method(print,geposan_preset)
 export(analyze)
diff --git a/R/ranking.R b/R/ranking.R
index e55917d..7898bc9 100644
--- a/R/ranking.R
+++ b/R/ranking.R
@@ -37,6 +37,62 @@ ranking <- function(analysis, weights) {
     )
 }
 
+#' S3 method for plotting a ranking.
+#'
+#' @param gene_sets A list of gene sets (containing vectors of gene IDs) that
+#'   will be highlighted in the plot.
+#' @param labels Labels for the gene sets.
+#'
+#' @seealso ranking()
+#'
+#' @export
+plot.geposan_ranking <- function(ranking, gene_sets = NULL, labels = NULL) {
+    if (!requireNamespace("plotly", quietly = TRUE)) {
+        stop("Please install \"plotly\" to use this function.")
+    }
+
+    plot <- plotly::plot_ly() |>
+        plotly::add_trace(
+            data = ranking,
+            x = ~rank,
+            y = ~score,
+            color = "All genes",
+            type = "scatter",
+            mode = "markers",
+            hoverinfo = "skip"
+        ) |>
+        plotly::layout(
+            xaxis = list(title = "Rank"),
+            yaxis = list(title = "Score")
+        )
+
+    if (length(gene_sets) > 0) {
+        # Take out the genes to be highlighted.
+        gene_set_data <- ranking[gene %chin% unlist(gene_sets)]
+
+        # Add labels for each gene set.
+        for (i in seq_along(gene_sets)) {
+            gene_set_data[gene %chin% gene_sets[[i]], label := labels[i]]
+        }
+
+        # Include gene information which will be used for laebling
+        gene_set_data <- merge(gene_set_data, genes, by.x = "gene", by.y = "id")
+
+        plot <- plot |> plotly::add_trace(
+            data = gene_set_data,
+            x = ~rank,
+            y = ~score,
+            color = ~label,
+            text = ~name,
+            type = "scatter",
+            mode = "markers",
+            marker = list(size = 20)
+        )
+    }
+
+    plot
+}
+
 #' Find the best weights to rank the results.
 #'
 #' This function finds the optimal parameters to [ranking()] that result in the
diff --git a/man/plot.geposan_ranking.Rd b/man/plot.geposan_ranking.Rd
new file mode 100644
index 0000000..3bfaa6b
--- /dev/null
+++ b/man/plot.geposan_ranking.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ranking.R
+\name{plot.geposan_ranking}
+\alias{plot.geposan_ranking}
+\title{S3 method for plotting a ranking.}
+\usage{
+\method{plot}{geposan_ranking}(ranking, gene_sets = NULL, labels = NULL)
+}
+\arguments{
+\item{gene_sets}{A list of gene sets (containing vectors of gene IDs) that
+will be highlighted in the plot.}
+
+\item{labels}{Labels for the gene sets.}
+}
+\description{
+S3 method for plotting a ranking.
+}
+\seealso{
+ranking()
+}