From 1bd5e41c8faac19311238d809d86ec835319ae38 Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Wed, 22 Jun 2022 19:34:39 +0200
Subject: [PATCH] Add additional information page

---
 R/server.R     |   2 ++
 R/sysdata.rda  | Bin 0 -> 3515 bytes
 R/ui.R         |  31 +++++++++++++++++++++++++++----
 scripts/gsea.R |   3 +++
 4 files changed, 32 insertions(+), 4 deletions(-)
 create mode 100644 R/sysdata.rda

diff --git a/R/server.R b/R/server.R
index 00600c3..18cd5d4 100644
--- a/R/server.R
+++ b/R/server.R
@@ -159,6 +159,8 @@ server <- function(input, output, session) {
       DT::formatRound("p_value", digits = 4) |>
       DT::formatPercentage(c("total_ratio", "query_ratio"), digits = 1)
   })
+
+  output$gsea_plot_ranking <- plotly::renderPlotly(gsea_plot_ranking)
 }
 
 #' Create a displayable data table from the gene results data.
diff --git a/R/sysdata.rda b/R/sysdata.rda
new file mode 100644
index 0000000000000000000000000000000000000000..c785d0cf64f0a8541f1f79d591fca193b2d9f600
GIT binary patch
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diff --git a/R/ui.R b/R/ui.R
index 9040149..b7e071f 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -141,10 +141,33 @@ ui <- function() {
         )
       ),
       tabPanel(
-        title = "Help"
-      ),
-      tabPanel(
-        title = "Publication"
+        title = "Additional information",
+        div(
+          class = "container",
+          h2("Number of interesting genes along the ranking"),
+          p(HTML(paste0(
+            "The notion of ubiquitous genes or housekeeping genes implies ",
+            "some kind of enrichment of important genes. Within groups of ",
+            "genes with certain biological associations, these genes should ",
+            "be overrepresented. We use GeneOntology terms as well as some ",
+            "other gene set sources to represent this concept. The following ",
+            "plot shows the number of associated terms for a non-overlapping ",
+            "sliding window of 500 genes along the ranking of ubiquity using ",
+            "our default parameters. The terms have been obtained using a ",
+            "gene set enrichment analysis with the tool ",
+            "<a href=\"https://biit.cs.ut.ee/gprofiler/gost\" ",
+            "target=\"_blank\">g:Profiler</a>. We observe that the most ",
+            "ubiquitous genes have many more known biological implications ",
+            "than any other bucket of genes. The genes of average ubiquity ",
+            "have almost no associations with GeneOntology terms. The number ",
+            "of associations rises again for the least ubiquitous genes."
+          ))),
+          p(HTML(paste0(
+            "Note: Click on the legend items to toggle single sources. A ",
+            "double-click will isolate a single source of interest."
+          ))),
+          plotly::plotlyOutput("gsea_plot_ranking", height = "600px")
+        )
       )
     )
   )
diff --git a/scripts/gsea.R b/scripts/gsea.R
index e0d0edb..6fb92ca 100644
--- a/scripts/gsea.R
+++ b/scripts/gsea.R
@@ -45,3 +45,6 @@ fig <- plotly::plot_ly() |>
   )
 
 plotly::save_image(fig, image_path, width = 1200, height = 800)
+
+gsea_plot_ranking <- fig
+usethis::use_data(gsea_plot_ranking, internal = TRUE, overwrite = TRUE)