Revert "proximity: Remove method"

This reverts commit ac9894e988.

NAMESPACE

@@ -22,6 +22,7 @@ export(plot_positions)
 export(plot_rankings)
 export(plot_scores)
 export(preset)
+export(proximity)
 export(ranking)
 export(result)
 export(species_adjacency)

R/method.R

@@ -37,7 +37,8 @@ all_methods <- function() {
         correlation(),
         neural(),
         adjacency(),
-        species_adjacency()
+        species_adjacency(),
+        proximity()
     )
 }
 

R/proximity.R

@@ -0,0 +1,39 @@
+#' Score the mean distance of genes to the telomeres across species.
+#'
+#' A score will be given to each gene such that 0.0 corresponds to the maximal
+#' mean distance across all genes and 1.0 corresponds to a distance of 0.
+#'
+#' @return An object of class `geposan_method`.
+#'
+#' @export
+proximity <- function() {
+    method(
+        id = "proximity",
+        name = "Proximity",
+        description = "Proximity to telomeres",
+        function(preset, progress) {
+            species_ids <- preset$species_ids
+            gene_ids <- preset$gene_ids
+
+            cached("proximity", c(species_ids, gene_ids), {
+                # Prefilter distances by species and gene.
+                data <- geposan::distances[
+                    species %chin% preset$species_ids &
+                        gene %chin% preset$gene_ids
+                ]
+
+                # Compute the score as described above.
+                data <- data[, .(mean_distance = mean(distance)), by = "gene"]
+                max_distance <- data[, max(mean_distance)]
+                data[, score := 1 - mean_distance / max_distance]
+
+                progress(1.0)
+
+                result(
+                    method = "proximity",
+                    scores = data[, .(gene, score)]
+                )
+            })
+        }
+    )
+}

man/proximity.Rd

@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/proximity.R
+\name{proximity}
+\alias{proximity}
+\title{Score the mean distance of genes to the telomeres across species.}
+\usage{
+proximity()
+}
+\value{
+An object of class \code{geposan_method}.
+}
+\description{
+A score will be given to each gene such that 0.0 corresponds to the maximal
+mean distance across all genes and 1.0 corresponds to a distance of 0.
+}