Version 1.1.0

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: geposanui
 Title: Graphical user interface for geposan
-Version: 1.0.1
+Version: 1.1.0
 Authors@R:
     person(
         "Elias",

R/app.R

@@ -91,7 +91,7 @@ ui <- function(options) {
       HTML(glue::glue(
         "<code>geposanui</code> version {packageVersion(\"geposanui\")}<br>",
         "GitHub: <a href=\"https://github.com/johrpan/geposanui/\" ",
-        "target=\"blank\">johrpan/geposan</a><br>",
+        "target=\"blank\">johrpan/geposanui</a><br>",
         "Citation: <a href=\"https://doi.org/10.1093/nargab/lqae037\" ",
         "target=\"blank\">10.1093/nargab/lqae037</a>"
       ))

R/comparison_editor.R

@@ -32,6 +32,18 @@ comparison_editor_ui <- function(id, options) {
         NS(id, "comparison_genes")
       ),
       gene_selector_ui(NS(id, "custom_genes"))
+    ),
+    tabsetPanel(
+      id = NS(id, "warning_panel"),
+      type = "hidden",
+      tabPanelBody(value = "hide"),
+      tabPanelBody(
+        value = "show",
+        div(
+          style = "color: orange; margin-bottom: 16px;",
+          htmlOutput(NS(id, "warnings"))
+        )
+      )
     )
   )
 }
@@ -49,18 +61,72 @@ comparison_editor_server <- function(id, preset, options) {
   moduleServer(id, function(input, output, session) {
     custom_gene_ids <- gene_selector_server("custom_genes")
 
+    comparison_warnings <- reactiveVal(character())
+    output$warnings <- renderUI({
+      HTML(paste(comparison_warnings(), collapse = "<br>"))
+    })
+
+    observe({
+      updateTabsetPanel(
+        session,
+        "warning_panel",
+        selected = if (is.null(comparison_warnings())) "hide" else "show"
+      )
+    })
+
     reactive({
-      if (input$comparison_genes == "Random genes") {
-        preset <- preset()
-        gene_pool <- preset$gene_ids
-        reference_gene_ids <- preset$reference_gene_ids
-        gene_pool <- gene_pool[!gene_pool %chin% reference_gene_ids]
+      new_warnings <- character()
+
+      preset <- preset()
+      gene_pool <- preset$gene_ids
+      reference_gene_ids <- preset$reference_gene_ids
+      gene_pool <- gene_pool[!gene_pool %chin% reference_gene_ids]
+
+      gene_ids <- if (input$comparison_genes == "Random genes") {
         gene_pool[sample(length(gene_pool), length(reference_gene_ids))]
       } else if (input$comparison_genes == "Your genes") {
         custom_gene_ids()
       } else {
         options$comparison_gene_sets[[input$comparison_genes]]
       }
+
+      excluded_reference_gene_ids <-
+        gene_ids[gene_ids %chin% reference_gene_ids]
+
+      if (length(excluded_reference_gene_ids) > 0) {
+        excluded_reference_genes <-
+          geposan::genes[id %chin% excluded_reference_gene_ids]
+        excluded_reference_genes[is.na(name), name := id]
+
+        new_warnings <- c(new_warnings, paste0(
+          "The following genes have been excluded because they are already ",
+          "part of the reference genes: ",
+          paste(
+            excluded_reference_genes$name,
+            collapse = ", "
+          )
+        ))
+      }
+
+      excluded_gene_ids <- gene_ids[!gene_ids %chin% gene_pool]
+
+      if (length(excluded_gene_ids) > 0) {
+        excluded_genes <-
+          geposan::genes[id %chin% excluded_gene_ids]
+        excluded_genes[is.na(name), name := id]
+
+        new_warnings <- c(new_warnings, paste0(
+          "The following genes are not present in the results: ",
+          paste(
+            excluded_genes$name,
+            collapse = ", "
+          )
+        ))
+      }
+
+      comparison_warnings(new_warnings)
+
+      gene_ids[!gene_ids %chin% reference_gene_ids & gene_ids %chin% gene_pool]
     })
   })
 }

R/details.R

@@ -86,19 +86,6 @@ details_server <- function(id, options, results) {
       "Percentile"
     )
 
-    output_data <- reactive({
-      filtered_results()[, ..columns][
-        ,
-        distance := paste0(
-          format(
-            round(distance / 1000000, digits = 2),
-            nsmall = 2,
-          ),
-          " Mbp"
-        )
-      ]
-    })
-
     output$download <- downloadHandler(
       filename = "geposan_filtered_results.csv",
       content = \(file) fwrite(filtered_results()[, ..columns], file = file),

R/preset_editor.R

@@ -102,8 +102,8 @@ preset_editor_ui <- function(id, options) {
         "reference genes to find patterns in their ",
         "chromosomal positions. If you would like to apply ",
         "this method for your own research, see ",
-        "<a href=\"https://code.johrpan.de/johrpan/geposanui/src/",
-        "branch/main/README.md\" target=\"_blank\">this page</a> for ",
+        "<a href=\"https://github.com/johrpan/geposanui/blob/main/README.md\" ",
+        "target=\"_blank\">this page</a> for ",
         "more information."
       ))
     }
@@ -196,7 +196,6 @@ preset_editor_server <- function(id, options) {
         ),
         warning = function(w) {
           new_warnings <<- c(new_warnings, w$message)
-
         }
       )
 

R/results.R

@@ -32,7 +32,31 @@ results_ui <- function(id, options) {
             plotly::plotlyOutput(
               NS(id, "rank_plot"),
               width = "100%",
-              height = "600px"
+              height = "500px"
+            )
+          ),
+          tabsetPanel(
+            id = NS(id, "comparison_results_panel"),
+            type = "hidden",
+            tabPanelBody(value = "hide"),
+            tabPanelBody(
+              value = "show",
+              div(
+                style = paste0(
+                  "display: flex; gap: 16px; align-items: center; ",
+                  "margin-top: 16px"
+                ),
+                div("Detailed results for the selected comparison genes"),
+                downloadButton(
+                  NS(id, "download_comparison_results"),
+                  "Download CSV",
+                  class = "btn-outline-primary"
+                )
+              ),
+              div(
+                style = "margin-top: 16px; margin-bottom: 8px;",
+                DT::DTOutput(NS(id, "comparison_results"))
+              )
             )
           )
         ),
@@ -245,6 +269,73 @@ results_server <- function(id, options, analysis) {
       geposan::plot_scores(ranking(), gene_sets = gene_sets)
     })
 
+    observe({
+      updateTabsetPanel(
+        session,
+        "comparison_results_panel",
+        selected = if (length(comparison_gene_ids()) > 0) "show" else "hide"
+      )
+    })
+
+    methods <- options$methods
+    method_ids <- sapply(methods, function(method) method$id)
+    method_names <- sapply(methods, function(method) method$name)
+
+    columns <- c(
+      "rank",
+      "gene",
+      "name",
+      "chromosome",
+      "distance",
+      method_ids,
+      "score",
+      "percentile"
+    )
+
+    column_names <- c(
+      "",
+      "Gene",
+      "",
+      "Chr.",
+      "Distance",
+      method_names,
+      "Score",
+      "Percentile"
+    )
+
+    results_filtered_comparison <- reactive({
+      results()[gene %chin% comparison_gene_ids()]
+    })
+
+    output$download_comparison_results <- downloadHandler(
+      filename = "geposan_results_custom.csv",
+      content = \(file) fwrite(
+        results_filtered_comparison()[, ..columns],
+        file = file
+      ),
+      contentType = "text/csv"
+    )
+
+    output$comparison_results <- DT::renderDT({
+      data <- results_filtered_comparison()[, ..columns]
+      data[, distance := glue::glue(
+        "{format(round(distance / 1000000, digits = 2), nsmall = 2)} Mbp"
+      )]
+
+      DT::datatable(
+        data,
+        rownames = FALSE,
+        colnames = column_names,
+        options = list(
+          rowCallback = js_link(),
+          columnDefs = list(list(visible = FALSE, targets = 2)),
+          pageLength = 25
+        )
+      ) |>
+        DT::formatRound(c(method_ids, "score"), digits = 4) |>
+        DT::formatPercentage("percentile", digits = 2)
+    })
+
     output$rankings_plot <- plotly::renderPlotly({
       preset <- preset()
 
@@ -360,7 +451,7 @@ results_server <- function(id, options, analysis) {
         preset()$reference_gene_ids
       )
 
-      comparison <- if (!is.null(comparison_gene_ids())) {
+      comparison <- if (length(comparison_gene_ids()) > 0) {
         geposan::compare(ranking(), comparison_gene_ids())
       }
 

inst/misc/style.css

@@ -28,6 +28,16 @@ h5 {
     font-weight: normal;
 }
 
+.navbar[data-bs-theme="light"] {
+    --bslib-navbar-light-bg: #1964BF;
+    --bs-navbar-color: rgba(255, 255, 255, 0.65);
+    --bs-navbar-hover-color: rgba(255, 255, 255, 0.8);
+    --bs-navbar-disabled-color: rgba(255, 255, 255, 0.3);
+    --bs-navbar-active-color: #fff;
+    --bs-navbar-brand-color: #fff;
+    --bs-navbar-brand-hover-color: #fff;
+}
+
 /* Fix slider inputs floating above dropdown menu */
 .irs--shiny .irs-bar {
     z-index: 1;