From c009bfa3719055a04b4bf2a4f6c44eab3c4b851c Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Mon, 15 Nov 2021 15:12:42 +0100
Subject: [PATCH] scatter plot: Move to geposan

---
 R/scatter_plot.R | 33 ---------------------------------
 R/server.R       | 34 +++++++++++++++++++++++++++-------
 R/ui.R           |  4 ++++
 3 files changed, 31 insertions(+), 40 deletions(-)
 delete mode 100644 R/scatter_plot.R

diff --git a/R/scatter_plot.R b/R/scatter_plot.R
deleted file mode 100644
index f10b13d..0000000
--- a/R/scatter_plot.R
+++ /dev/null
@@ -1,33 +0,0 @@
-# Draw a scatter plot containing gene positions.
-#
-# @param results Results from [`process_input()`].
-# @param species Species to be displayed.
-# @param genes Genes to be displayed.
-scatter_plot <- function(results, species, genes) {
-    species_ids <- species[, id]
-
-    data <- merge(
-        genes[, .(id, name)],
-        geposan::distances[species %in% species_ids],
-        by.x = "id", by.y = "gene"
-    )
-
-    data[name == "", name := "Unknown"]
-
-    plotly::plot_ly(
-        data = data,
-        x = ~species,
-        y = ~distance,
-        color = ~id,
-        name = ~name,
-        type = "scatter",
-        mode = "markers"
-    ) |> plotly::layout(
-        xaxis = list(
-            title = "Species",
-            tickvals = species_ids,
-            ticktext = species[, name]
-        ),
-        yaxis = list(title = "Distance to telomeres [Bp]")
-    )
-}
diff --git a/R/server.R b/R/server.R
index c01f2fd..da2f1a6 100644
--- a/R/server.R
+++ b/R/server.R
@@ -106,13 +106,27 @@ server <- function(input, output, session) {
     })
 
     output$scatter <- plotly::renderPlotly({
-        results <- results_filtered()
+        preset <- preset()
 
-        gene_ids <- results[input$genes_rows_selected, gene]
-        genes <- genes[id %chin% gene_ids]
-        species <- species[id %chin% preset()$species_ids]
+        gene_sets <- list(preset$reference_gene_ids)
+        labels <- c("Reference genes")
 
-        scatter_plot(results, species, genes)
+        comparison_gene_ids <- results_filtered()[
+            input$genes_rows_selected,
+            gene
+        ]
+
+        if (length(comparison_gene_ids) >= 1) {
+            gene_sets <- c(gene_sets, list(comparison_gene_ids))
+            labels <- c(labels, "Comparison genes")
+        }
+
+        geposan::plot_positions(
+            preset$species_ids,
+            gene_sets = gene_sets,
+            labels = labels,
+            use_positions = input$use_positions
+        )
     })
 
     output$assessment_synopsis <- renderText({
@@ -157,7 +171,10 @@ server <- function(input, output, session) {
         gene_sets <- list(preset()$reference_gene_ids)
         labels <- c("Reference genes")
 
-        comparison_gene_ids <- results()[input$genes_rows_selected, gene]
+        comparison_gene_ids <- results_filtered()[
+            input$genes_rows_selected,
+            gene
+        ]
 
         if (length(comparison_gene_ids) >= 1) {
             gene_sets <- c(gene_sets, list(comparison_gene_ids))
@@ -176,7 +193,10 @@ server <- function(input, output, session) {
         gene_sets <- list(preset()$reference_gene_ids)
         labels <- c("Reference genes")
 
-        comparison_gene_ids <- results()[input$genes_rows_selected, gene]
+        comparison_gene_ids <- results_filtered()[
+            input$genes_rows_selected,
+            gene
+        ]
 
         if (length(comparison_gene_ids) >= 1) {
             gene_sets <- c(gene_sets, list(comparison_gene_ids))
diff --git a/R/ui.R b/R/ui.R
index 11a234b..afa5aa8 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -31,6 +31,10 @@ ui <- fluidPage(
                 ),
                 tabPanel(
                     "Positions",
+                    checkboxInput(
+                        "use_positions",
+                        "Show positions instead of distances"
+                    ),
                     plotly::plotlyOutput(
                         "scatter",
                         width = "100%",