Reorganize source files and generalize presets

process/process.R

@@ -0,0 +1,58 @@
+library(data.table)
+
+source("process/util.R")
+
+# Load input data
+
+source("process/input.R")
+
+species <- run_cached("inputs/species", retrieve_species)
+genes <- run_cached("inputs/genes", retrieve_genes)
+
+distances <- run_cached(
+    "inputs/distances",
+    retrieve_distances,
+    species[, id],
+    genes[, id]
+)
+
+genes <- merge(
+    genes,
+    distances[, .(n_species = .N), by = "gene"],
+    by.x = "id",
+    by.y = "gene"
+)
+
+source("process/methods.R")
+source("process/presets.R")
+
+#' Apply all methods with the specified preset without caching.
+process_priv <- function(preset) {
+    results <- data.table(gene = genes[, id])
+
+    for (method in methods) {
+        method_results <- method$fn(distances, genes[, id], preset)
+        setnames(method_results, "score", method$id)
+
+        results <- merge(
+            results,
+            method_results
+        )
+    }
+
+    results
+}
+
+#' Apply all methods with the specified preset.
+#'
+#' The result will be cached by the preset's hash and restored from cache, if
+#' possible. The return value is a `data.table` with one row for each gene
+#' identified by it's ID (`gene` column). The additional columns contain the
+#' resulting per method and are named after the method IDs.
+process <- function(preset) {
+    run_cached(
+        sprintf("results/%s", rlang::hash(preset)),
+        process_priv,
+        preset
+    )
+}