Remove global methods data

DESCRIPTION

@@ -15,12 +15,14 @@ Description: This package provides a graphical user interface for analyzing
 License: AGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Imports:
+    bslib,
     data.table,
     disgenet2r,
     DT,
     geposan,
+    glue,
     gprofiler2,
     plotly,
     purrr,

R/data.R

@@ -1,8 +0,0 @@
-# All available methods from [geposan] and additional information on them.
-methods <- geposan::all_methods()
-
-# IDs of methods for geposan.
-method_ids <- sapply(methods, function(method) method$id)
-
-# Names of methods for geposan.
-method_names <- sapply(methods, function(method) method$name)

R/methods.R

@@ -21,7 +21,7 @@ methods_ui <- function(id) {
         "Customize weights" = "custom"
       )
     ),
-    lapply(methods, function(method) {
+    lapply(geposan::all_methods(), function(method) {
       verticalLayout(
         checkboxInput(
           NS(id, method$id),
@@ -52,7 +52,7 @@ methods_ui <- function(id) {
 methods_server <- function(id, analysis, comparison_gene_ids) {
   moduleServer(id, function(input, output, session) {
     # Observe each method's enable button and synchronise the slider state.
-    lapply(methods, function(method) {
+    lapply(geposan::all_methods(), function(method) {
       observeEvent(input[[method$id]], {
         shinyjs::toggleState(
           sprintf("%s_weight", method$id),
@@ -89,7 +89,7 @@ methods_server <- function(id, analysis, comparison_gene_ids) {
 
         included_methods <- NULL
 
-        for (method in methods) {
+        for (method in geposan::all_methods()) {
           if (input[[method$id]]) {
             included_methods <- c(included_methods, method$id)
           }
@@ -105,7 +105,7 @@ methods_server <- function(id, analysis, comparison_gene_ids) {
     }) |> bindCache(
       analysis(),
       optimization_gene_ids(),
-      sapply(methods, function(method) input[[method$id]]),
+      sapply(geposan::all_methods(), function(method) input[[method$id]]),
       input$optimization_target
     )
 
@@ -114,7 +114,7 @@ methods_server <- function(id, analysis, comparison_gene_ids) {
 
       if (length(optimization_gene_ids()) < 1 |
         input$optimization_target == "custom") {
-        for (method in methods) {
+        for (method in geposan::all_methods()) {
           if (input[[method$id]]) {
             weight <- input[[sprintf("%s_weight", method$id)]]
             weights[[method$id]] <- weight

R/results.R

@@ -51,6 +51,10 @@ results_server <- function(id, filtered_results) {
       )
     })
 
+    methods <- geposan::all_methods()
+    method_ids <- sapply(methods, function(method) method$id)
+    method_names <- sapply(methods, function(method) method$name)
+
     columns <- c(
       "rank",
       "gene",