Reformat to use two spaces for tabs

R/server.R

@@ -1,43 +1,43 @@
 #' Server implementing the main user interface.
 #' @noRd
 server <- function(input, output) {
-    ranked_data <- reactive({
-        total_weight <- abs(input$above_zero) +
-            abs(input$above_median) +
-            abs(input$above_95) +
-            abs(input$mean_expression) +
-            abs(input$sd_expression)
+  ranked_data <- reactive({
+    total_weight <- abs(input$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 <- data.table::copy(ubigen::genes)
 
-        data[, score :=
-            (input$above_zero * above_zero +
-                input$above_95 * above_95 +
-                input$above_median * above_median +
-                input$mean_expression * mean_expression_normalized +
-                input$sd_expression * sd_expression_normalized) /
-                total_weight]
+    data[, score :=
+      (input$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]
 
-        data.table::setorder(data, -score)
-        data[, rank := .I]
-        data[, percentile := 1 - rank / max(rank)]
+    data.table::setorder(data, -score)
+    data[, rank := .I]
+    data[, percentile := 1 - rank / max(rank)]
 
-        data
-    })
+    data
+  })
 
-    output$scores_plot <- plotly::renderPlotly(scores_plot(ranked_data()))
+  output$scores_plot <- plotly::renderPlotly(scores_plot(ranked_data()))
 
-    output$selected_genes <- DT::renderDataTable({
-        selected_points <- plotly::event_data("plotly_selected")
+  output$selected_genes <- DT::renderDataTable({
+    selected_points <- plotly::event_data("plotly_selected")
 
-        data <- if (is.null(selected_points)) {
-            ranked_data()
-        } else {
-            ranked_data()[rank %in% selected_points$x]
-        }
+    data <- if (is.null(selected_points)) {
+      ranked_data()
+    } else {
+      ranked_data()[rank %in% selected_points$x]
+    }
 
-        genes_table(data)
-    })
+    genes_table(data)
+  })
 }
 
 #' Create plot showing the distribution of scores using `plotly`.
@@ -49,95 +49,95 @@ server <- function(input, output) {
 #' @return A `plotly` figure for rendering.
 #' @noRd
 scores_plot <- function(ranked_data, ranks = 1000) {
-    data <- if (is.null(ranks)) {
-        ranked_data
-    } else {
-        ranked_data[1:ranks]
-    }
+  data <- if (is.null(ranks)) {
+    ranked_data
+  } else {
+    ranked_data[1:ranks]
+  }
 
-    ranks_label <- if (is.null(ranks)) {
-        "Ranks"
-    } else {
-        glue::glue("Ranks (1 to {ranks})")
-    }
+  ranks_label <- if (is.null(ranks)) {
+    "Ranks"
+  } else {
+    glue::glue("Ranks (1 to {ranks})")
+  }
 
-    plotly::plot_ly() |>
-        plotly::add_markers(
-            data = data,
-            x = ~rank,
-            y = ~score,
-            text = ~hgnc_name,
-            customdata = ~percentile,
-            hovertemplate = paste0(
-                "<b>%{text}</b><br>",
-                "Rank: %{x}<br>",
-                "Score: %{y:.2}<br>",
-                "Percentile: %{customdata:.2%}",
-                "<extra></extra>"
-            )
-        ) |>
-        plotly::layout(
-            xaxis = list(title = ranks_label),
-            yaxis = list(title = "Score"),
-            clickmode = "event+select",
-            dragmode = "select"
-        )
+  plotly::plot_ly() |>
+    plotly::add_markers(
+      data = data,
+      x = ~rank,
+      y = ~score,
+      text = ~hgnc_name,
+      customdata = ~percentile,
+      hovertemplate = paste0(
+        "<b>%{text}</b><br>",
+        "Rank: %{x}<br>",
+        "Score: %{y:.2}<br>",
+        "Percentile: %{customdata:.2%}",
+        "<extra></extra>"
+      )
+    ) |>
+    plotly::layout(
+      xaxis = list(title = ranks_label),
+      yaxis = list(title = "Score"),
+      clickmode = "event+select",
+      dragmode = "select"
+    )
 }
 
 #' Create a displayable data table from the gene results data.
 #' @noRd
 genes_table <- function(data) {
-    data <- data[, .(
-        "Gene" = glue::glue_data(
-            data,
-            "<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
-            "?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
-        ),
-        "Rank" = rank,
-        "Percentile" = percentile,
-        "Score" = score,
-        "Median" = median_expression,
-        "Mean" = mean_expression,
-        "Standard deviation" = sd_expression,
-        "Expressed" = above_zero,
-        "Above median" = above_median,
-        "Above 95%" = above_95
-    )]
+  data <- data[, .(
+    "Gene" = glue::glue_data(
+      data,
+      "<a href=\"https://www.ensembl.org/Homo_sapiens/Gene/Summary",
+      "?db=core;g={gene}\" target=\"_blank\">{hgnc_name}</a>"
+    ),
+    "Rank" = rank,
+    "Percentile" = percentile,
+    "Score" = score,
+    "Median" = median_expression,
+    "Mean" = mean_expression,
+    "Standard deviation" = sd_expression,
+    "Expressed" = above_zero,
+    "Above median" = above_median,
+    "Above 95%" = above_95
+  )]
 
-    DT::datatable(
-        data,
-        options = list(
-            buttons = list(
-                list(
-                    extend = "copy",
-                    text = "Copy to clipboard"
-                ),
-                list(
-                    extend = "csv",
-                    text = "Download CSV"
-                )
-            ),
-            dom = "fBrtip",
-            pageLength = 100
+  DT::datatable(
+    data,
+    options = list(
+      buttons = list(
+        list(
+          extend = "copy",
+          text = "Copy to clipboard"
         ),
-        rownames = FALSE,
-        escape = FALSE,
-        selection = "none",
-        extensions = "Buttons"
+        list(
+          extend = "csv",
+          text = "Download CSV"
+        )
+      ),
+      dom = "fBrtip",
+      pageLength = 100
+    ),
+    rownames = FALSE,
+    escape = FALSE,
+    selection = "none",
+    extensions = "Buttons"
+  ) |>
+    DT::formatPercentage(
+      c(
+        "Percentile",
+        "Score",
+        "Expressed",
+        "Above median",
+        "Above 95%"
+      ),
+      digits = 2,
     ) |>
-        DT::formatPercentage(
-            c(
-                "Percentile",
-                "Score",
-                "Expressed",
-                "Above median",
-                "Above 95%"
-            ),
-            digits = 2,
-        ) |>
-        DT::formatRound(c(
-            "Median",
-            "Mean",
-            "Standard deviation"
-        ))
+    DT::formatRound(c(
+      "Median",
+      "Mean",
+      "Standard deviation"
+    ))
 }