From 20faaea93d65b2cd5ef33accd69a3861115188ed Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Mon, 30 May 2022 20:08:54 +0200
Subject: [PATCH] Add overview

---
 DESCRIPTION |  2 +-
 R/plots.R   | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 R/server.R  | 45 +-----------------------------------
 R/ui.R      |  3 +++
 R/utils.R   |  3 +--
 5 files changed, 72 insertions(+), 47 deletions(-)
 create mode 100644 R/plots.R

diff --git a/DESCRIPTION b/DESCRIPTION
index bda25ce..15ec548 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -15,7 +15,7 @@ Description: This package contains precomputed data including comparisons in
 License: AGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Depends:
     R (>= 2.10)
 LazyData: true
diff --git a/R/plots.R b/R/plots.R
new file mode 100644
index 0000000..fb21ee9
--- /dev/null
+++ b/R/plots.R
@@ -0,0 +1,66 @@
+#' Create a plot showing an overview over the provided ranking.
+#'
+#' @param ranked_data The ranking to visualize.
+#' @param sample_proportion Proportion of rows to use as the shown sample.
+#'
+#' @return A `plotly` figure.
+#' @noRd
+overview_plot <- function(ranked_data, sample_proportion = 0.05) {
+  plotly::plot_ly() |>
+    plotly::add_lines(
+      data = ranked_data[sample(
+        nrow(ranked_data),
+        sample_proportion * nrow(ranked_data)
+      )],
+      x = ~rank,
+      y = ~score
+    ) |>
+    plotly::layout(
+      xaxis = list(title = "Ranks"),
+      yaxis = list(title = "Score")
+    )
+}
+
+#' Create plot showing the distribution of scores using `plotly`.
+#'
+#' @param ranked_data Data on genes with precomputed ranks.
+#' @param ranks How may ranks the x-axis should include. If this parameter is
+#'   `NULL`, all ranks will be shown.
+#'
+#' @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]
+  }
+
+  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"
+    )
+}
diff --git a/R/server.R b/R/server.R
index 52b1db4..10c847e 100644
--- a/R/server.R
+++ b/R/server.R
@@ -25,6 +25,7 @@ server <- function(input, output) {
     data
   })
 
+  output$overview_plot <- plotly::renderPlotly(overview_plot(ranked_data()))
   output$scores_plot <- plotly::renderPlotly(scores_plot(ranked_data()))
 
   output$selected_genes <- DT::renderDataTable({
@@ -40,50 +41,6 @@ server <- function(input, output) {
   })
 }
 
-#' Create plot showing the distribution of scores using `plotly`.
-#'
-#' @param ranked_data Data on genes with precomputed ranks.
-#' @param ranks How may ranks the x-axis should include. If this parameter is
-#'   `NULL`, all ranks will be shown.
-#'
-#' @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]
-  }
-
-  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"
-    )
-}
-
 #' Create a displayable data table from the gene results data.
 #' @noRd
 genes_table <- function(data) {
diff --git a/R/ui.R b/R/ui.R
index e562f53..5f53b08 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -90,6 +90,9 @@ ui <- function() {
         mainPanel(
           width = 9,
           h3("Distribution of scores"),
+          h4("Overview"),
+          plotly::plotlyOutput("overview_plot", height = "200px"),
+          h4("Focus on top genes"),
           div(paste0(
             "Click or drag within the figure to select genes of ",
             "interest."
diff --git a/R/utils.R b/R/utils.R
index e8d2ef6..c58fbf3 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,5 +1,4 @@
-#' Various things that should be imported into the package namespace.
-#'
+# Various things that should be imported into the package namespace.
 #' @importFrom data.table :=
 #' @importFrom data.table .BY
 #' @importFrom data.table .EACHI