From 7e53015168889baf86945d880f96f826f6bdd0a0 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Tue, 17 May 2022 21:48:30 +0200
Subject: [PATCH] Add chromosomal positions plot

---
 NAMESPACE                      |  1 +
 R/plots.R                      | 41 +++++++++++++++++++++++++++++++++-
 man/plot_scores_by_position.Rd | 22 ++++++++++++++++++
 3 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100644 man/plot_scores_by_position.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 841e328..3f1aefe 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -21,6 +21,7 @@ export(plot_chromosomes)
 export(plot_positions)
 export(plot_rankings)
 export(plot_scores)
+export(plot_scores_by_position)
 export(preset)
 export(proximity)
 export(ranking)
diff --git a/R/plots.R b/R/plots.R
index 6c41cf7..98b9b50 100644
--- a/R/plots.R
+++ b/R/plots.R
@@ -46,7 +46,8 @@ plot_positions <- function(species_ids, gene_sets) {
             ),
             yaxis = list(title = "Distance to telomeres [Bp]"),
             bargap = 0.9
-        ) |> plotly::add_bars(
+        ) |>
+        plotly::add_bars(
             data = species_max_distance,
             x = ~species,
             y = ~max_distance,
@@ -379,3 +380,41 @@ plot_chromosomes <- function(ranking) {
             yaxis = list(title = "Mean score")
         )
 }
+
+#' Plot scores in relation to chromosomal position of genes.
+#'
+#' @param ranking The ranking to visualize.
+#' @param chromosome_name The chromosome to visualize.
+#'
+#' @return A `plotly` figure.
+#' @seealso ranking()
+#'
+#' @export
+plot_scores_by_position <- function(ranking, chromosome_name) {
+    if (!requireNamespace("plotly", quietly = TRUE)) {
+        stop("Please install \"plotly\" to use this function.")
+    }
+
+    chromosome_name_ <- chromosome_name
+
+    data <- merge(
+        ranking,
+        geposan::distances[
+            species == "hsapiens" &
+                chromosome_name == chromosome_name_
+        ],
+        by = "gene"
+    )
+
+    plotly::plot_ly() |>
+        plotly::add_markers(
+            data = data,
+            x = ~start_position,
+            y = ~score,
+            hoverinfo = "skip"
+        ) |>
+        plotly::layout(
+            xaxis = list(title = "Position (Bp)"),
+            yaxis = list(title = "Score")
+        )
+}
diff --git a/man/plot_scores_by_position.Rd b/man/plot_scores_by_position.Rd
new file mode 100644
index 0000000..1124359
--- /dev/null
+++ b/man/plot_scores_by_position.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plots.R
+\name{plot_scores_by_position}
+\alias{plot_scores_by_position}
+\title{Plot scores in relation to chromosomal position of genes.}
+\usage{
+plot_scores_by_position(ranking, chromosome_name)
+}
+\arguments{
+\item{ranking}{The ranking to visualize.}
+
+\item{chromosome_name}{The chromosome to visualize.}
+}
+\value{
+A \code{plotly} figure.
+}
+\description{
+Plot scores in relation to chromosomal position of genes.
+}
+\seealso{
+ranking()
+}