From 365cf13dcbcb5c27ee44ac70419b09ebcc649e86 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 21 Oct 2021 11:43:34 +0200
Subject: [PATCH] Add more optimization targets

---
 R/methods.R | 24 +++++++++++++++++-------
 R/server.R  |  6 +++++-
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index e14db7b..fb49fd0 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -4,11 +4,6 @@ methods_ui <- function(id) {
 
     verticalLayout(
         h3("Methods"),
-        actionButton(
-            NS(id, "optimize_button"),
-            "Find optimal weights",
-            icon = icon("check-double")
-        ),
         div(style = "margin-top: 16px"),
         lapply(methods, function(method) {
             verticalLayout(
@@ -30,7 +25,21 @@ methods_ui <- function(id) {
                     value = initial_weight
                 )
             )
-        })
+        }),
+        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",
+            class = "btn-primary"
+        )
     )
 }
 
@@ -54,7 +63,8 @@ methods_server <- function(id, analysis) {
             weights <- geposan::optimize_weights(
                 analysis(),
                 method_ids,
-                genes_tpe_old
+                genes_tpe_old,
+                target = input$target
             )
 
             for (method_id in method_ids) {
diff --git a/R/server.R b/R/server.R
index 44df265..cb5edaf 100644
--- a/R/server.R
+++ b/R/server.R
@@ -160,19 +160,23 @@ server <- function(input, output, session) {
                 digits = 1
             ))
 
+            min_rank <- as.character(reference_results[, min(rank)])
             max_rank <- as.character(reference_results[, max(rank)])
         } else {
             mean_rank <- "Unknown"
+            min_rank <- "Unknown"
             max_rank <- "Unknown"
         }
 
         sprintf(
             "Included reference genes: %i/%i<br> \
             Mean rank of reference genes: %s<br> \
-            Maximum rank of reference genes: %s",
+            First rank of reference genes: %s<br> \
+            Last rank of reference genes: %s",
             included_reference_count,
             total_reference_count,
             mean_rank,
+            min_rank,
             max_rank
         )
     })