From 47b8d7a1f03f88df3924a87411994d5d199ede2e Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Mon, 23 May 2022 11:39:30 +0200
Subject: [PATCH] Show all chromosomes in position plot by default

---
 R/server.R | 8 +++++++-
 R/ui.R     | 5 ++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/R/server.R b/R/server.R
index 41da59a..19fc351 100644
--- a/R/server.R
+++ b/R/server.R
@@ -189,9 +189,15 @@ server <- function(options) {
                 )
             }
 
+            chromosome <- if (input$positions_plot_chromosome_name == "all") {
+                NULL
+            } else {
+                input$positions_plot_chromosome_name
+            }
+
             geposan::plot_scores_by_position(
                 ranking(),
-                input$positions_plot_chromosome_name,
+                chromosome_name = chromosome,
                 gene_sets = gene_sets
             )
         })
diff --git a/R/ui.R b/R/ui.R
index 587dc94..70dc0e1 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -73,7 +73,10 @@ ui <- function(options) {
                                     selectInput(
                                         "positions_plot_chromosome_name",
                                         label = NULL,
-                                        choices = chromosome_choices()
+                                        choices = c(
+                                            list("All chromosomes" = "all"),
+                                            chromosome_choices()
+                                        )
                                     ),
                                     plotly::plotlyOutput(
                                         "positions_plot",