From b5957262a3368cd38a556ef31c272f7e39129da3 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Mon, 15 Nov 2021 09:35:47 +0100
Subject: [PATCH] Use plots from geposan

---
 R/rank_plot.R | 53 ---------------------------------------------------
 R/server.R    | 17 +++++++++++++----
 R/ui.R        |  8 ++++++++
 3 files changed, 21 insertions(+), 57 deletions(-)
 delete mode 100644 R/rank_plot.R

diff --git a/R/rank_plot.R b/R/rank_plot.R
deleted file mode 100644
index f9a847a..0000000
--- a/R/rank_plot.R
+++ /dev/null
@@ -1,53 +0,0 @@
-# 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.
-# @param max_rank Last rank of the included genes.
-rank_plot <- function(results, reference_gene_ids, max_rank) {
-    plot <- plotly::plot_ly() |> plotly::add_trace(
-        data = results,
-        x = ~rank,
-        y = ~score,
-        name = "All genes",
-        type = "scatter",
-        mode = "line",
-        hoverinfo = "skip"
-    ) |> plotly::add_trace(
-        data = results[gene %chin% reference_gene_ids],
-        x = ~rank,
-        y = ~score,
-        color = ~gene,
-        name = ~name,
-        width = 10,
-        type = "bar"
-    )  |> plotly::layout(
-        xaxis = list(title = "Ranks"),
-        yaxis = list(title = "Score")
-    )
-
-    first_not_included_rank <- max_rank + 1
-    last_rank <- results[, .N]
-
-    if (first_not_included_rank <= last_rank) {
-        plot <- plot |> plotly::layout(
-            shapes = list(
-                type = "rect",
-                fillcolor = "black",
-                opacity = 0.1,
-                x0 = first_not_included_rank,
-                x1 = last_rank,
-                y0 = 0.0,
-                y1 = 1.0
-            )
-        )
-    }
-
-    plot
-}
diff --git a/R/server.R b/R/server.R
index 788ce5d..51d5b97 100644
--- a/R/server.R
+++ b/R/server.R
@@ -154,10 +154,19 @@ server <- function(input, output, session) {
     })
 
     output$rank_plot <- plotly::renderPlotly({
-        rank_plot(
-            results(),
-            preset()$reference_gene_ids,
-            results_filtered()[, max(rank)]
+        geposan::plot_scores(
+            ranking(),
+            gene_sets = list(preset()$reference_gene_ids),
+            labels = "TPE-OLD genes",
+            max_rank = results_filtered()[, max(rank)]
+        )
+    })
+
+    output$boxplot <- plotly::renderPlotly({
+        geposan::plot_boxplot(
+            ranking(),
+            gene_sets = list(preset()$reference_gene_ids),
+            labels = "TPE-OLD genes"
         )
     })
 
diff --git a/R/ui.R b/R/ui.R
index 95f6d39..d637b9e 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -48,6 +48,14 @@ ui <- fluidPage(
                             height = "600px"
                         )
                     ),
+                    div(
+                        style = "margin-top: 16px",
+                        plotly::plotlyOutput(
+                            "boxplot",
+                            width = "100%",
+                            height = "600px"
+                        )
+                    ),
                 ),
                 tabPanel(
                     "Analysis",