From b4d758ff03f5be5bb8d26ad8751fe5b70d47da4a Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 12 May 2022 13:03:13 +0200
Subject: [PATCH] Include more features

---
 R/server.R |  8 ++++++--
 R/ui.R     | 60 ++++++++++++++++++++++++++++++++++++++++++++++++------
 2 files changed, 60 insertions(+), 8 deletions(-)

diff --git a/R/server.R b/R/server.R
index e5b152d..fa9a735 100644
--- a/R/server.R
+++ b/R/server.R
@@ -2,14 +2,18 @@
 #' @noRd
 server <- function(input, output) {
     ranked_data <- reactive({
-        total_weight <- abs(input$above_median) +
+        total_weight <- abs(input$above_zero) +
+            abs(input$above_median) +
+            abs(input$above_95) +
             abs(input$mean_expression) +
             abs(input$sd_expression)
 
         data <- data.table::copy(ubigen::genes)
 
         data[, score :=
-            (input$above_median * above_median +
+            (input$above_zero * above_zero +
+                input$above_95 * above_95 +
+                input$above_median * above_median +
                 input$mean_expression * mean_expression_normalized +
                 input$sd_expression * sd_expression_normalized) /
                 total_weight]
diff --git a/R/ui.R b/R/ui.R
index ab29e5c..f2852c5 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -13,18 +13,60 @@ ui <- function() {
             sidebarLayout(
                 sidebarPanel(
                     width = 3,
-                    h3("Criteria"),
+                    h3("Features"),
                     sliderInput(
-                        "above_median",
-                        "Expressed above median",
+                        "above_zero",
+                        verticalLayout(
+                            strong("Expressed"),
+                            paste0(
+                                "Percentage of samples in which the gene is ",
+                                "expressed."
+                            )
+                        ),
                         min = -1.0,
                         max = 1.0,
                         step = 0.01,
-                        value = 1.0
+                        value = 0.33
+                    ),
+                    sliderInput(
+                        "above_median",
+                        verticalLayout(
+                            strong("Expressed above median"),
+                            paste0(
+                                "Percentage of samples that express the gene ",
+                                "more than the median of expression within ",
+                                "that sample."
+                            )
+                        ),
+                        min = -1.0,
+                        max = 1.0,
+                        step = 0.01,
+                        value = 0.33
+                    ),
+                    sliderInput(
+                        "above_95",
+                        verticalLayout(
+                            strong("Expressed above 95%"),
+                            paste0(
+                                "Percentage of samples that express the gene ",
+                                "more than the 95. percentile of expression ",
+                                "within that sample."
+                            )
+                        ),
+                        min = -1.0,
+                        max = 1.0,
+                        step = 0.01,
+                        value = 0.33
                     ),
                     sliderInput(
                         "mean_expression",
-                        "Mean expression",
+                        verticalLayout(
+                            strong("Mean expression"),
+                            div(paste0(
+                                "Average of the gene's expression across all ",
+                                "samples."
+                            ))
+                        ),
                         min = -1.0,
                         max = 1.0,
                         step = 0.01,
@@ -32,7 +74,13 @@ ui <- function() {
                     ),
                     sliderInput(
                         "sd_expression",
-                        "Standard deviation",
+                        verticalLayout(
+                            strong("Standard deviation"),
+                            paste0(
+                                "Standard deviation of the gene's expression ",
+                                "across all samples."
+                            )
+                        ),
                         min = -1.0,
                         max = 1.0,
                         step = 0.01,