Rename method proximity to distance

R/method_distance.R

@@ -0,0 +1,54 @@
+#' 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 id Unique ID for the method and its results.
+#' @param name Human readable name for the method.
+#' @param description Method description.
+#' @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
+distance <- function(id = "distance",
+                      name = "Distance",
+                      description = "Distance to telomeres",
+                      summarize = stats::median) {
+  method(
+    id = id,
+    name = name,
+    description = description,
+    function(preset, progress) {
+      species_ids <- preset$species_ids
+      gene_ids <- preset$gene_ids
+
+      cached("distance", 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 := combined_distance / max(combined_distance)]
+
+        progress(1.0)
+
+        result(
+          method = "distance",
+          scores = data[, .(gene, score)],
+          details = list(data = data)
+        )
+      })
+    }
+  )
+}