From c26e4ff4a3ca378d50fa0b378d36ee16673520e1 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Mon, 11 Oct 2021 11:14:08 +0200
Subject: [PATCH] Add option to penalize missing values

---
 server.R | 18 +++++++++++++++---
 ui.R     |  4 ++++
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/server.R b/server.R
index 13eb005..3e924cc 100644
--- a/server.R
+++ b/server.R
@@ -58,10 +58,22 @@ server <- function(input, output) {
         results[, score := clusteriness_factor * clusteriness +
             correlation_factor * correlation + neural_factor * neural]
 
-        # Apply the cut-off score & the required number of species.
+        # Exclude genes with too few species.
+        results <- results[n_species >= input$n_species]
 
-        results <- results[n_species >= input$n_species &
-            score >= input$cutoff / 100]
+        # Penalize missing species.
+        if (input$penalize) {
+            species_count <- if (input$species == "all") {
+                nrow(species)
+            } else {
+                length(species_ids_replicative)
+            }
+
+            results <- results[, score := score * n_species / species_count]
+        }
+
+        # Apply the cut-off score.
+        results <- results[score >= input$cutoff / 100]
 
         # Order the results based on their score. The resulting index will be
         # used as the "rank".
diff --git a/ui.R b/ui.R
index 0e1ac75..ca5f818 100644
--- a/ui.R
+++ b/ui.R
@@ -57,6 +57,10 @@ ui <- fluidPage(
                 max = 100,
                 step = 1,
                 value = 50
+            ),
+            checkboxInput(
+                "penalize",
+                "Penalize missing values"
             )
         ),
         wellPanel(