Convert to R package

R/server.R

@@ -0,0 +1,204 @@
+# Java script function to replace gene IDs with Ensembl gene links.
+js_link <- DT::JS("function(row, data) {
+    let id = data[1];
+    var name = data[2];
+    if (!name) name = 'Unknown';
+    let url = `https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=${id}`;
+    $('td:eq(1)', row).html(`<a href=\"${url}\" target=\"_blank\">${name}</a>`);
+}")
+
+server <- function(input, output, session) {
+    # Show the customized slider for setting the required number of species.
+    output$n_species_slider <- renderUI({
+        sliderInput(
+            "n_species",
+            "Required number of species per gene",
+            min = 0,
+            max = if (input$species == "all") {
+                nrow(species)
+            } else {
+                length(species_ids_replicative)
+            },
+            step = 1,
+            value = 10
+        )
+    })
+
+    # Compute the results according to the preset.
+    analysis <- reactive({
+        # Select the preset.
+        preset <- if (input$species == "all") {
+            preset_all_species
+        } else {
+            preset_replicative_species
+        }
+
+        # Perform the analysis cached based on the preset's hash.
+        results <- withProgress(
+            message = "Analyzing genes",
+            value = 0.0, {
+                run_cached(
+                    rlang::hash(preset),
+                    geposan::analyze,
+                    preset,
+                    function(progress) {
+                        setProgress(progress)
+                    }
+                )
+            }
+        )
+
+        # Add all gene information to the results.
+        results <- merge(
+            results,
+            genes,
+            by.x = "gene",
+            by.y = "id"
+        )
+
+        # Count included species from the preset per gene.
+        genes_n_species <- geposan::distances[
+            species %chin% preset$species_ids,
+            .(n_species = .N),
+            by = "gene"
+        ]
+
+        setkey(genes_n_species, gene)
+
+        # Exclude genes with too few species.
+        results[genes_n_species[gene, n_species] >= input$n_species]
+    })
+
+    # Rank the results.
+    results <- methods_server("methods", analysis)
+
+    # Apply the cut-off score to the ranked results.
+    results_filtered <- reactive({
+        results()[score >= input$cutoff / 100]
+    })
+
+    output$genes <- DT::renderDT({
+        method_ids <- sapply(methods, function(method) method$id)
+        method_names <- sapply(methods, function(method) method$name)
+        columns <- c("rank", "gene", "name", "chromosome", method_ids, "score")
+        column_names <- c("", "Gene", "", "Chromosome", method_names, "Score")
+
+        dt <- DT::datatable(
+            results_filtered()[, ..columns],
+            rownames = FALSE,
+            colnames = column_names,
+            style = "bootstrap",
+            fillContainer = TRUE,
+            extensions = "Scroller",
+            options = list(
+                rowCallback = js_link,
+                columnDefs = list(list(visible = FALSE, targets = 2)),
+                deferRender = TRUE,
+                scrollY = 200,
+                scroller = TRUE
+            )
+        )
+
+        DT::formatPercentage(dt, c(method_ids, "score"), digits = 1)
+    })
+
+    output$copy <- renderUI({
+        results <- results_filtered()
+
+        gene_ids <- results[, gene]
+        names <- results[name != "", name]
+
+        genes_text <- paste(gene_ids, collapse = "\n")
+        names_text <- paste(names, collapse = "\n")
+
+        splitLayout(
+            cellWidths = "auto",
+            rclipboard::rclipButton(
+                "copy_ids_button",
+                "Copy gene IDs",
+                genes_text,
+                icon = icon("clipboard")
+            ),
+            rclipboard::rclipButton(
+                "copy_names_button",
+                "Copy gene names",
+                names_text,
+                icon = icon("clipboard")
+            )
+        )
+    })
+
+    output$scatter <- plotly::renderPlotly({
+        results <- results_filtered()
+
+        gene_ids <- results[input$genes_rows_selected, gene]
+        genes <- genes[id %chin% gene_ids]
+
+        species <- if (input$species == "all") {
+            species
+        } else {
+            species[replicative == TRUE]
+        }
+
+        scatter_plot(results, species, genes)
+    })
+
+    output$assessment_synopsis <- renderText({
+        reference_gene_ids <- genes[suggested | verified == TRUE, id]
+
+        included_reference_count <- results_filtered()[
+            gene %chin% reference_gene_ids,
+            .N
+        ]
+
+        reference_results <- results()[gene %chin% reference_gene_ids]
+        total_reference_count <- nrow(reference_results)
+
+        if (total_reference_count > 0) {
+            mean_rank <- as.character(round(
+                reference_results[, mean(rank)],
+                digits = 1
+            ))
+
+            max_rank <- as.character(reference_results[, max(rank)])
+        } else {
+            mean_rank <- "Unknown"
+            max_rank <- "Unknown"
+        }
+
+        sprintf(
+            "Included reference genes: %i/%i<br> \
+            Mean rank of reference genes: %s<br> \
+            Maximum rank of reference genes: %s",
+            included_reference_count,
+            total_reference_count,
+            mean_rank,
+            max_rank
+        )
+    })
+
+    output$rank_plot <- plotly::renderPlotly({
+        rank_plot(
+            results(),
+            genes[suggested | verified == TRUE, id],
+            input$cutoff / 100
+        )
+    })
+
+    output$gost <- plotly::renderPlotly({
+        if (input$enable_gost) {
+            result <- gprofiler2::gost(
+                results_filtered()[, gene],
+                ordered_query = TRUE
+            )
+
+            gprofiler2::gostplot(
+                result,
+                capped = FALSE,
+                interactive = TRUE
+            )
+        } else {
+            NULL
+        }
+    })
+}