From d2d1e09858de663b6ba5eebac55696ff205490d6 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Fri, 19 Nov 2021 15:38:46 +0100
Subject: [PATCH] Move optimization to preset editor

---
 R/methods.R       | 65 ++++++++++++++++++-----------------------------
 R/preset_editor.R | 15 +++++++++--
 2 files changed, 38 insertions(+), 42 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index cb7ab2c..4daa723 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -23,18 +23,9 @@ methods_ui <- function(id) {
                 )
             )
         }),
-        radioButtons(
-            NS(id, "target"),
-            "Optimization target",
-            choices = list(
-                "Mean rank of reference genes" = "mean",
-                "First rank of reference genes" = "min",
-                "Last rank of reference genes" = "max"
-            )
-        ),
         actionButton(
-            NS(id, "optimize_button"),
-            "Optimize weights",
+            NS(id, "reset_button"),
+            "Reset weights",
             class = "btn-primary"
         )
     )
@@ -47,33 +38,6 @@ methods_ui <- function(id) {
 # @return A reactive containing the weighted results.
 methods_server <- function(id, analysis) {
     moduleServer(id, function(input, output, session) {
-        observeEvent(input$optimize_button, {
-            analysis <- analysis()
-            method_ids <- NULL
-
-            # Only include activated methods.
-            for (method in methods) {
-                if (input[[method$id]]) {
-                    method_ids <- c(method_ids, method$id)
-                }
-            }
-
-            weights <- geposan::optimal_weights(
-                analysis,
-                method_ids,
-                analysis$preset$reference_gene_ids,
-                target = input$target
-            )
-
-            for (method_id in method_ids) {
-                updateSliderInput(
-                    session,
-                    sprintf("%s_weight", method_id),
-                    value = weights[[method_id]]
-                )
-            }
-        })
-
         # Observe each method's enable button and synchronise the slider state.
         lapply(methods, function(method) {
             observeEvent(input[[method$id]],
@@ -84,9 +48,30 @@ methods_server <- function(id, analysis) {
             )
         })
 
-        reactive({
-            # Take the actual weights from the sliders.
+        observeEvent(
+            { # nolint
+                analysis()
+                input$reset_button
+            },
+            { # nolint
+                for (method in methods) {
+                    updateCheckboxInput(
+                        session,
+                        method$id,
+                        value = TRUE
+                    )
 
+                    updateSliderInput(
+                        session,
+                        sprintf("%s_weight", method$id),
+                        value = analysis()$weights[[method$id]]
+                    )
+                }
+            },
+            ignoreNULL = FALSE
+        )
+
+        reactive({
             weights <- NULL
 
             for (method in methods) {
diff --git a/R/preset_editor.R b/R/preset_editor.R
index 72f2059..acc4eee 100644
--- a/R/preset_editor.R
+++ b/R/preset_editor.R
@@ -61,6 +61,15 @@ preset_editor_ui <- function(id) {
                 )
             )
         ),
+        selectInput(
+            NS(id, "optimization_target"),
+            "Optimization target",
+            choices = list(
+                "Mean rank of reference genes" = "mean",
+                "First rank of reference genes" = "min",
+                "Last rank of reference genes" = "max"
+            )
+        ),
         tabsetPanel(
             id = NS(id, "apply_panel"),
             type = "hidden",
@@ -89,7 +98,8 @@ preset_editor_server <- function(id) {
             methods = method_ids,
             species_ids = species[replicative == TRUE, id],
             gene_ids = genes$id,
-            reference_gene_ids = genes[suggested | verified == TRUE, id]
+            reference_gene_ids = genes[suggested | verified == TRUE, id],
+            optimization_target = "mean"
         ))
 
         observeEvent(input$species, {
@@ -145,7 +155,8 @@ preset_editor_server <- function(id) {
                 methods = method_ids,
                 species_ids = species_ids,
                 gene_ids = genes$id,
-                reference_gene_ids = reference_gene_ids
+                reference_gene_ids = reference_gene_ids,
+                optimization_target = input$optimization_target
             )
         })