From 48c903f8c786742ebdc51564bdda5c426c789e0d Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Thu, 2 Dec 2021 17:22:27 +0100
Subject: [PATCH] Update plots

---
 R/server.R | 62 +++++++++++++++++++-----------------------------------
 R/ui.R     |  6 +-----
 2 files changed, 23 insertions(+), 45 deletions(-)

diff --git a/R/server.R b/R/server.R
index 5146536..a4b252f 100644
--- a/R/server.R
+++ b/R/server.R
@@ -92,26 +92,17 @@ server <- function(input, output, session) {
 
     output$scatter <- plotly::renderPlotly({
         preset <- preset()
-
-        gene_sets <- list(preset$reference_gene_ids)
-        labels <- c("Reference genes")
-
-        comparison_gene_ids <- results_filtered()[
-            input$genes_rows_selected,
-            gene
-        ]
+        gene_sets <- list("Reference genes" = preset$reference_gene_ids)
+        comparison_gene_ids <- comparison_gene_ids()
 
         if (length(comparison_gene_ids) >= 1) {
-            gene_sets <- c(gene_sets, list(comparison_gene_ids))
-            labels <- c(labels, "Comparison genes")
+            gene_sets <- c(
+                gene_sets,
+                list("Comparison genes" = comparison_gene_ids)
+            )
         }
 
-        geposan::plot_positions(
-            preset$species_ids,
-            gene_sets = gene_sets,
-            labels = labels,
-            use_positions = input$use_positions
-        )
+        geposan::plot_positions(preset$species_ids, gene_sets)
     })
 
     output$assessment_synopsis <- renderText({
@@ -153,46 +144,37 @@ server <- function(input, output, session) {
     })
 
     output$rank_plot <- plotly::renderPlotly({
-        gene_sets <- list(preset()$reference_gene_ids)
-        labels <- c("Reference genes")
-
-        comparison_gene_ids <- results_filtered()[
-            input$genes_rows_selected,
-            gene
-        ]
+        preset <- preset()
+        gene_sets <- list("Reference genes" = preset$reference_gene_ids)
+        comparison_gene_ids <- comparison_gene_ids()
 
         if (length(comparison_gene_ids) >= 1) {
-            gene_sets <- c(gene_sets, list(comparison_gene_ids))
-            labels <- c(labels, "Comparison genes")
+            gene_sets <- c(
+                gene_sets,
+                list("Comparison genes" = comparison_gene_ids)
+            )
         }
 
         geposan::plot_scores(
             ranking(),
             gene_sets = gene_sets,
-            labels = labels,
             max_rank = results_filtered()[, max(rank)]
         )
     })
 
     output$boxplot <- plotly::renderPlotly({
-        gene_sets <- list(preset()$reference_gene_ids)
-        labels <- c("Reference genes")
-
-        comparison_gene_ids <- results_filtered()[
-            input$genes_rows_selected,
-            gene
-        ]
+        preset <- preset()
+        gene_sets <- list("Reference genes" = preset$reference_gene_ids)
+        comparison_gene_ids <- comparison_gene_ids()
 
         if (length(comparison_gene_ids) >= 1) {
-            gene_sets <- c(gene_sets, list(comparison_gene_ids))
-            labels <- c(labels, "Comparison genes")
+            gene_sets <- c(
+                gene_sets,
+                list("Comparison genes" = comparison_gene_ids)
+            )
         }
 
-        geposan::plot_boxplot(
-            ranking(),
-            gene_sets = gene_sets,
-            labels = labels
-        )
+        geposan::plot_boxplot(ranking(), gene_sets)
     })
 
     output$chromosome_plot <- plotly::renderPlotly({
diff --git a/R/ui.R b/R/ui.R
index f628cc3..ec37cbe 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -22,11 +22,7 @@ ui <- fluidPage(
                     )
                 ),
                 tabPanel(
-                    "Positions",
-                    checkboxInput(
-                        "use_positions",
-                        "Show positions instead of distances"
-                    ),
+                    "Input Data",
                     plotly::plotlyOutput(
                         "scatter",
                         width = "100%",