Add initial controls to the explore page

R/server.R

@@ -1,10 +1,34 @@
 #' Server implementing the main user interface.
 #' @noRd
 server <- function(input, output) {
-    output$all_data <- DT::renderDataTable({
-        data <- ubigen::genes[, .(
+    output$ranked_data <- DT::renderDataTable({
+        total_weight <- abs(input$above_median) +
+            abs(input$mean_expression) +
+            abs(input$sd_expression)
+
+        data <- data.table::copy(ubigen::genes)
+
+        data[, score :=
+            (input$above_median * above_median +
+                input$mean_expression * mean_expression_normalized +
+                input$sd_expression * sd_expression_normalized) /
+                total_weight]
+
+        data.table::setorder(data, -score)
+        data[, rank := .I]
+
+        genes_table(data)
+    })
+
+    output$all_data <- DT::renderDataTable(genes_table(ubigen::genes))
+}
+
+#' Create a displayable data table from the gene results data.
+#' @noRd
+genes_table <- function(data) {
+    data <- data[, .(
         "Gene" = glue::glue_data(
-                ubigen::genes,
+            data,
             "<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
             "?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
         ),
@@ -25,17 +49,19 @@ server <- function(input, output) {
         rownames = FALSE,
         escape = FALSE
     ) |>
-            DT::formatPercentage(c(
+        DT::formatPercentage(
+            c(
                 "Score",
                 "Expressed",
                 "Above 50 TPM",
                 "Above median",
                 "Above 95%"
-            )) |>
+            ),
+            digits = 2,
+        ) |>
         DT::formatRound(c(
             "Median",
             "Mean",
             "Standard deviation"
         ))
-    })
 }

R/ui.R

@@ -13,9 +13,35 @@ ui <- function() {
             sidebarLayout(
                 sidebarPanel(
                     width = 3,
+                    h3("Criteria"),
+                    sliderInput(
+                        "above_median",
+                        "Expressed above median",
+                        min = -1.0,
+                        max = 1.0,
+                        step = 0.01,
+                        value = 1.0
+                    ),
+                    sliderInput(
+                        "mean_expression",
+                        "Mean expression",
+                        min = -1.0,
+                        max = 1.0,
+                        step = 0.01,
+                        value = 1.0
+                    ),
+                    sliderInput(
+                        "sd_expression",
+                        "Standard deviation",
+                        min = -1.0,
+                        max = 1.0,
+                        step = 0.01,
+                        value = -1.0
+                    )
                 ),
                 mainPanel(
                     width = 9,
+                    DT::dataTableOutput("ranked_data")
                 )
             )
         ),