proximity: Use median distance by default

R/method_proximity.R

@@ -0,0 +1,48 @@
+#' Score the distance of genes to the telomeres across species.
+#'
+#' A score will be given to each gene such that 0.0 corresponds to the maximal
+#' distance across all genes and 1.0 corresponds to a distance of 0.
+#'
+#' @param summarize A function for combining the different proximities into one
+#'   metric. By default, [stats::median()] is used. Other suggested options
+#'   include [min()] and [mean()].
+#'
+#' @return An object of class `geposan_method`.
+#'
+#' @export
+proximity <- function(summarize = stats::median) {
+    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[,
+                    .(combined_distance = as.double(summarize(distance))),
+                    by = "gene"
+                ]
+
+                # Normalize scores.
+                data[, score := 1 - combined_distance / max(combined_distance)]
+
+                progress(1.0)
+
+                result(
+                    method = "proximity",
+                    scores = data[, .(gene, score)],
+                    details = list(data = data)
+                )
+            })
+        }
+    )
+}