Add optimizer and buttons to disable methods

optimize.R

@@ -0,0 +1,34 @@
+#' Find the best weights to rank the data.
+#'
+#' This function ranks the provided data table based on a weighted score
+#' computed from the specified `columns`. It tries to find the optimal weights
+#' that result in a ranking, where the mean rank of the given reference genes
+#' is as high as possible.
+#'
+#' @param data Input data including the columns.
+#' @param colums Columns containing the separate scores between 0.0 and 1.0.
+#' @param reference_gene_ids IDs of the reference genes within the input data.
+#'
+#' @returns Vector of optimal column weights adding up to 1.0.
+optimize_weights <- function(data, columns, reference_gene_ids) {
+    #' Compute the mean rank of the reference genes when applying the weights.
+    mean_rank <- function(weights) {
+        data <- copy(data)
+        data[, score := 0.0]
+
+        for (i in seq_along(columns)) {
+            column <- columns[i]
+            weighted <- weights[i] * data[, ..column]
+            data[, score := score + weighted]
+        }
+
+        setorder(data, -score)
+        data[, rank := .I]
+
+        data[gene %chin% reference_gene_ids, mean(rank)]
+    }
+
+    weights <- optim(rep(1.0, length(columns)), mean_rank)$par
+    total_weight <- sum(weights)
+    weights / total_weight
+}