From 527ba01cc9adbbe103df606ea4cd420b316658fc Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Fri, 15 Oct 2021 13:16:51 +0200
Subject: [PATCH] Add rank plot

---
 rank_plot.R | 36 ++++++++++++++++++++++++++++++++++++
 server.R    |  6 ++++++
 ui.R        |  6 ++++++
 3 files changed, 48 insertions(+)
 create mode 100644 rank_plot.R

diff --git a/rank_plot.R b/rank_plot.R
new file mode 100644
index 0000000..efea50e
--- /dev/null
+++ b/rank_plot.R
@@ -0,0 +1,36 @@
+library(data.table)
+library(plotly)
+
+#' Draw a plot displaying the rank of reference genes.
+#'
+#' The input table should contain the following columns:
+#'
+#'  - `gene` Gene IDs of genes to display.
+#'  - `name` Name of genes to display.
+#'  - `score` Score of the genes.
+#'  - `rank` Rank of the genes based on the score.
+#'
+#' @param results Results to display.
+#' @param reference_gene_ids IDs of reference genes.
+rank_plot <- function(results, reference_gene_ids) {
+    plot <- plot_ly() |> add_trace(
+        data = results,
+        x = ~rank,
+        y = ~score,
+        name = "All genes",
+        type = "scatter",
+        mode = "line",
+        hoverinfo = "skip"
+    ) |> add_trace(
+        data = results[gene %chin% reference_gene_ids],
+        x = ~rank,
+        y = ~score,
+        color = ~gene,
+        name = ~name,
+        width = 10,
+        type = "bar"
+    ) |> layout(
+        xaxis = list(title = "Ranks"),
+        yaxis = list(title = "Score")
+    )
+}
\ No newline at end of file
diff --git a/server.R b/server.R
index 59070a1..c6ba4f9 100644
--- a/server.R
+++ b/server.R
@@ -6,6 +6,7 @@ library(rclipboard)
 library(shiny)
 
 source("init.R")
+source("rank_plot.R")
 source("scatter_plot.R")
 
 #' Java script function to replace gene IDs with Ensembl gene links.
@@ -83,6 +84,11 @@ server <- function(input, output) {
         results[, rank := .I]
     })
 
+    output$rank_plot <- renderPlotly({
+        results <- results()
+        rank_plot(results, genes[suggested | verified == TRUE, id])
+    })
+
     output$genes <- renderDT({
         method_ids <- sapply(methods, function(method) method$id)
         method_names <- sapply(methods, function(method) method$name)
diff --git a/ui.R b/ui.R
index 5e72b39..147f048 100644
--- a/ui.R
+++ b/ui.R
@@ -48,6 +48,12 @@ ui <- fluidPage(
             ),
         ),
         mainPanel(
+            h3("Gene ranks"),
+            plotlyOutput(
+                "rank_plot",
+                width = "100%",
+                height = "600px"
+            ),
             h3("Results"),
             textOutput("synposis"),
             div(