From a1807691d5e0cd725277af23c73943e1193b824a Mon Sep 17 00:00:00 2001
From: Elias Projahn <elias@johrpan.de>
Date: Wed, 17 Nov 2021 22:58:55 +0100
Subject: [PATCH] Move species count to preset

---
 R/methods.R       | 22 +++++++++-------------
 R/preset_editor.R | 38 +++++++++++++++++++++++++++++---------
 R/server.R        | 13 +------------
 R/ui.R            |  8 --------
 4 files changed, 39 insertions(+), 42 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index 4a44f72..cb7ab2c 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -43,11 +43,9 @@ methods_ui <- function(id) {
 # Construct server for the methods editor.
 #
 # @param analysis The reactive containing the results to be weighted.
-# @param min_n_species A reactive containing the minimum number of species to
-#   require for genes to be included in the ranking.
 #
 # @return A reactive containing the weighted results.
-methods_server <- function(id, analysis, min_n_species) {
+methods_server <- function(id, analysis) {
     moduleServer(id, function(input, output, session) {
         observeEvent(input$optimize_button, {
             analysis <- analysis()
@@ -64,8 +62,7 @@ methods_server <- function(id, analysis, min_n_species) {
                 analysis,
                 method_ids,
                 analysis$preset$reference_gene_ids,
-                target = input$target,
-                min_n_species = min_n_species()
+                target = input$target
             )
 
             for (method_id in method_ids) {
@@ -79,9 +76,12 @@ methods_server <- function(id, analysis, min_n_species) {
 
         # Observe each method's enable button and synchronise the slider state.
         lapply(methods, function(method) {
-            observeEvent(input[[method$id]], {
-                shinyjs::toggleState(sprintf("%s_weight", method$id))
-            }, ignoreInit = TRUE)
+            observeEvent(input[[method$id]],
+                { # nolint
+                    shinyjs::toggleState(sprintf("%s_weight", method$id))
+                },
+                ignoreInit = TRUE
+            )
         })
 
         reactive({
@@ -96,11 +96,7 @@ methods_server <- function(id, analysis, min_n_species) {
                 }
             }
 
-            geposan::ranking(
-                analysis(),
-                weights,
-                min_n_species = min_n_species()
-            )
+            geposan::ranking(analysis(), weights)
         })
     })
 }
diff --git a/R/preset_editor.R b/R/preset_editor.R
index 72f2059..dded591 100644
--- a/R/preset_editor.R
+++ b/R/preset_editor.R
@@ -35,6 +35,14 @@ preset_editor_ui <- function(id) {
                 )
             )
         ),
+        sliderInput(
+            NS(id, "n_species"),
+            "Required number of species per gene",
+            min = 0,
+            max = 18,
+            step = 1,
+            value = 10
+        ),
         selectInput(
             NS(id, "reference_genes"),
             "Reference genes",
@@ -89,6 +97,7 @@ preset_editor_server <- function(id) {
             methods = method_ids,
             species_ids = species[replicative == TRUE, id],
             gene_ids = genes$id,
+            min_n_species = 10,
             reference_gene_ids = genes[suggested | verified == TRUE, id]
         ))
 
@@ -108,6 +117,24 @@ preset_editor_server <- function(id) {
             }
         })
 
+        species_ids <- reactive({
+            if (input$species == "replicative") {
+                species[replicative == TRUE, id]
+            } else if (input$species == "all") {
+                species$id
+            } else {
+                input$custom_species
+            }
+        })
+
+        observeEvent(species_ids(), {
+            updateSliderInput(
+                session,
+                "n_species",
+                max = length(species_ids())
+            )
+        })
+
         observeEvent(input$reference_genes, {
             if (input$reference_genes == "custom") {
                 updateTabsetPanel(
@@ -125,14 +152,6 @@ preset_editor_server <- function(id) {
         })
 
         new_preset <- reactive({
-            species_ids <- if (input$species == "replicative") {
-                species[replicative == TRUE, id]
-            } else if (input$species == "all") {
-                species$id
-            } else {
-                input$custom_species
-            }
-
             reference_gene_ids <- if (input$reference_genes == "tpeold") {
                 genes[verified | suggested == TRUE, id]
             } else if (input$reference_genes == "verified") {
@@ -143,8 +162,9 @@ preset_editor_server <- function(id) {
 
             geposan::preset(
                 methods = method_ids,
-                species_ids = species_ids,
+                species_ids = species_ids(),
                 gene_ids = genes$id,
+                min_n_species = input$n_species,
                 reference_gene_ids = reference_gene_ids
             )
         })
diff --git a/R/server.R b/R/server.R
index da2f1a6..6f0bb70 100644
--- a/R/server.R
+++ b/R/server.R
@@ -10,15 +10,6 @@ js_link <- DT::JS("function(row, data) {
 server <- function(input, output, session) {
     preset <- preset_editor_server("preset_editor")
 
-    observe({
-        species_count <- length(preset()$species_ids)
-        updateSliderInput(
-            session,
-            "n_species",
-            max = species_count
-        )
-    })
-
     # Compute the results according to the preset.
     analysis <- reactive({
         preset <- preset()
@@ -37,10 +28,8 @@ server <- function(input, output, session) {
         analysis
     })
 
-    min_n_species <- reactive(input$n_species)
-
     # Rank the results.
-    ranking <- methods_server("methods", analysis, min_n_species)
+    ranking <- methods_server("methods", analysis)
 
     # Add gene information to the results.
     results <- reactive({
diff --git a/R/ui.R b/R/ui.R
index afa5aa8..891a79d 100644
--- a/R/ui.R
+++ b/R/ui.R
@@ -7,14 +7,6 @@ ui <- fluidPage(
             width = 3,
             preset_editor_ui("preset_editor"),
             filters_ui("filters"),
-            sliderInput(
-                "n_species",
-                "Required number of species per gene",
-                min = 0,
-                max = 18,
-                step = 1,
-                value = 10
-            ),
             methods_ui("methods")
         ),
         mainPanel(