mirror of
https://github.com/johrpan/geposanui.git
synced 2025-10-26 11:17:24 +01:00
Reindent code to use just two spaces
This commit is contained in:
parent
47b8d7a1f0
commit
13b5efc1e3
10 changed files with 1000 additions and 999 deletions
556
R/server.R
556
R/server.R
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@ -12,291 +12,291 @@ js_link <- DT::JS("function(row, data) {
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#' @param options Global application options.
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#' @noRd
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server <- function(options) {
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function(input, output, session) {
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input_reactives <- input_page_server("input_page", options)
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preset <- input_reactives$preset
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comparison_gene_ids <- input_reactives$comparison_gene_ids
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function(input, output, session) {
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input_reactives <- input_page_server("input_page", options)
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preset <- input_reactives$preset
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comparison_gene_ids <- input_reactives$comparison_gene_ids
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observe({
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updateNavbarPage(
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session,
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"main_page",
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selected = "Results"
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)
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}) |> bindEvent(preset(), ignoreInit = TRUE)
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observe({
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updateNavbarPage(
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session,
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"main_page",
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selected = "Results"
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)
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}) |> bindEvent(preset(), ignoreInit = TRUE)
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# Compute the results according to the preset.
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analysis <- reactive({
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withProgress(
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message = "Analyzing genes",
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value = 0.0,
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{ # nolint
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geposan::analyze(
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preset(),
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progress = function(progress) {
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setProgress(progress)
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},
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include_results = FALSE
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)
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}
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)
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}) |> bindCache(preset())
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# Compute the results according to the preset.
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analysis <- reactive({
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withProgress(
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message = "Analyzing genes",
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value = 0.0,
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{ # nolint
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geposan::analyze(
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preset(),
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progress = function(progress) {
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setProgress(progress)
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},
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include_results = FALSE
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)
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}
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)
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}) |> bindCache(preset())
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# Rank the results.
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ranking <- methods_server("methods", analysis, comparison_gene_ids)
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# Rank the results.
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ranking <- methods_server("methods", analysis, comparison_gene_ids)
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genes_with_distances <- merge(
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geposan::genes,
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geposan::distances[species == "hsapiens"],
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by.x = "id",
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by.y = "gene"
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genes_with_distances <- merge(
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geposan::genes,
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geposan::distances[species == "hsapiens"],
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by.x = "id",
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by.y = "gene"
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)
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# Add gene information to the results.
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results <- reactive({
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merge(
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ranking(),
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genes_with_distances,
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by.x = "gene",
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by.y = "id",
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sort = FALSE
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)
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})
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# Apply the filters.
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results_filtered <- filters_server("filters", results)
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# Server for the detailed results panel.
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results_server("results", results_filtered)
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output$rank_plot <- plotly::renderPlotly({
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preset <- preset()
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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# Add gene information to the results.
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results <- reactive({
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merge(
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ranking(),
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genes_with_distances,
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by.x = "gene",
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by.y = "id",
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sort = FALSE
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geposan::plot_scores(
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ranking(),
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gene_sets = gene_sets,
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max_rank = results_filtered()[, max(rank)]
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)
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})
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output$rankings_plot <- plotly::renderPlotly({
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preset <- preset()
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rankings <- list()
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methods <- preset$methods
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all <- ranking()
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for (method in methods) {
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weights <- list()
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weights[[method$id]] <- 1.0
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rankings[[method$name]] <- geposan::ranking(all, weights)
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}
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rankings[["Combined"]] <- all
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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geposan::plot_rankings(rankings, gene_sets)
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})
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output$comparison_text <- renderUI({
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reference <- geposan::compare(
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ranking(),
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preset()$reference_gene_ids
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)
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comparison <- if (!is.null(comparison_gene_ids())) {
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geposan::compare(ranking(), comparison_gene_ids())
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}
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num <- function(x, digits) {
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format(
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round(x, digits = digits),
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nsmall = digits,
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scientific = FALSE
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)
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}
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comparison_text <- function(name, comparison) {
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glue::glue(
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"The {name} have a mean score of ",
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"<b>{num(comparison$mean_score, 4)}</b> ",
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"resulting in a mean rank of ",
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"<b>{num(comparison$mean_rank, 1)}</b>. ",
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"This corresponds to a percent rank of ",
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"<b>{num(100 * comparison$mean_percentile, 2)}%</b>. ",
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"A Wilcoxon rank sum test with the hypothesis of higher ",
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"than usual scores gives a p-value of ",
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"<b>{num(comparison$p_value, 4)}</b>."
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)
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}
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reference_div <- div(HTML(
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comparison_text("reference genes", reference)
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))
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if (!is.null(comparison)) {
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div(
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reference_div,
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div(HTML(comparison_text("comparison genes", comparison)))
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)
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} else {
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reference_div
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}
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})
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output$boxplot <- plotly::renderPlotly({
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preset <- preset()
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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geposan::plot_boxplot(ranking(), gene_sets)
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})
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output$positions_plot <- plotly::renderPlotly({
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preset <- preset()
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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chromosome <- if (input$positions_plot_chromosome_name == "all") {
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NULL
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} else {
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input$positions_plot_chromosome_name
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}
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geposan::plot_scores_by_position(
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ranking(),
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chromosome_name = chromosome,
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gene_sets = gene_sets
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)
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})
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gost <- reactive({
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withProgress(
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message = "Querying g:Profiler",
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value = 0.0,
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{ # nolint
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setProgress(0.2)
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gprofiler2::gost(results_filtered()[, gene])
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}
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)
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})
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output$gost_plot <- plotly::renderPlotly({
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gprofiler2::gostplot(
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gost(),
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capped = FALSE,
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interactive = TRUE
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)
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})
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output$gost_details <- DT::renderDT({
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data <- data.table(gost()$result)
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setorder(data, p_value)
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data[, total_ratio := term_size / effective_domain_size]
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data[, query_ratio := intersection_size / query_size]
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data <- data[, .(
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source,
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term_name,
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total_ratio,
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query_ratio,
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p_value
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)]
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dt <- DT::datatable(
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data,
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rownames = FALSE,
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colnames = c(
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"Source",
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"Term",
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"Total ratio",
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"Query ratio",
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"p-value"
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),
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options = list(
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pageLength = 25
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)
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)
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dt <- DT::formatRound(dt, "p_value", digits = 4)
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dt <- DT::formatPercentage(
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dt,
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c("total_ratio", "query_ratio"),
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digits = 1
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)
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})
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output$disgenet <- DT::renderDT({
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withProgress(
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message = "Querying DisGeNET",
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value = 0.0,
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{ # nolint
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setProgress(0.2)
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gene_names <- results_filtered()[, name]
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gene_names <- unique(gene_names[gene_names != ""])
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diseases <- suppressMessages(
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disgenet2r::disease_enrichment(gene_names)
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)
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data <- data.table(diseases@qresult)
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data <- data[, .(Description, Ratio, BgRatio, pvalue)]
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setorder(data, pvalue)
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dt <- DT::datatable(
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data,
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rownames = FALSE,
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colnames = c(
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"Disease",
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"Query ratio",
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"Total ratio",
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"p-value"
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),
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options = list(
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pageLength = 25
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)
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})
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)
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# Apply the filters.
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results_filtered <- filters_server("filters", results)
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dt <- DT::formatRound(dt, "pvalue", digits = 4)
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# Server for the detailed results panel.
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results_server("results", results_filtered)
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output$rank_plot <- plotly::renderPlotly({
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preset <- preset()
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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geposan::plot_scores(
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ranking(),
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gene_sets = gene_sets,
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max_rank = results_filtered()[, max(rank)]
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)
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})
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output$rankings_plot <- plotly::renderPlotly({
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preset <- preset()
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rankings <- list()
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methods <- preset$methods
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all <- ranking()
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for (method in methods) {
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weights <- list()
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weights[[method$id]] <- 1.0
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rankings[[method$name]] <- geposan::ranking(all, weights)
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}
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rankings[["Combined"]] <- all
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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geposan::plot_rankings(rankings, gene_sets)
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})
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output$comparison_text <- renderUI({
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reference <- geposan::compare(
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ranking(),
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preset()$reference_gene_ids
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)
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comparison <- if (!is.null(comparison_gene_ids())) {
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geposan::compare(ranking(), comparison_gene_ids())
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}
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num <- function(x, digits) {
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format(
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round(x, digits = digits),
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nsmall = digits,
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scientific = FALSE
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)
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}
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comparison_text <- function(name, comparison) {
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glue::glue(
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"The {name} have a mean score of ",
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"<b>{num(comparison$mean_score, 4)}</b> ",
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"resulting in a mean rank of ",
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"<b>{num(comparison$mean_rank, 1)}</b>. ",
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"This corresponds to a percent rank of ",
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"<b>{num(100 * comparison$mean_percentile, 2)}%</b>. ",
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"A Wilcoxon rank sum test with the hypothesis of higher ",
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"than usual scores gives a p-value of ",
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"<b>{num(comparison$p_value, 4)}</b>."
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)
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}
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reference_div <- div(HTML(
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comparison_text("reference genes", reference)
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))
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if (!is.null(comparison)) {
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div(
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reference_div,
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div(HTML(comparison_text("comparison genes", comparison)))
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)
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} else {
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reference_div
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}
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})
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output$boxplot <- plotly::renderPlotly({
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preset <- preset()
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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geposan::plot_boxplot(ranking(), gene_sets)
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})
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output$positions_plot <- plotly::renderPlotly({
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preset <- preset()
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gene_sets <- list("Reference genes" = preset$reference_gene_ids)
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comparison_gene_ids <- comparison_gene_ids()
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if (length(comparison_gene_ids) >= 1) {
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gene_sets <- c(
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gene_sets,
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list("Comparison genes" = comparison_gene_ids)
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)
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}
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chromosome <- if (input$positions_plot_chromosome_name == "all") {
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NULL
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} else {
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input$positions_plot_chromosome_name
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}
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geposan::plot_scores_by_position(
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ranking(),
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chromosome_name = chromosome,
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gene_sets = gene_sets
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)
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})
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gost <- reactive({
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withProgress(
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message = "Querying g:Profiler",
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value = 0.0,
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{ # nolint
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setProgress(0.2)
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gprofiler2::gost(results_filtered()[, gene])
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}
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)
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})
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output$gost_plot <- plotly::renderPlotly({
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gprofiler2::gostplot(
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gost(),
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capped = FALSE,
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interactive = TRUE
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)
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})
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output$gost_details <- DT::renderDT({
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data <- data.table(gost()$result)
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setorder(data, p_value)
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data[, total_ratio := term_size / effective_domain_size]
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data[, query_ratio := intersection_size / query_size]
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data <- data[, .(
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source,
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term_name,
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total_ratio,
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query_ratio,
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p_value
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)]
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dt <- DT::datatable(
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data,
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rownames = FALSE,
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colnames = c(
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"Source",
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"Term",
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"Total ratio",
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"Query ratio",
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"p-value"
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),
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options = list(
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pageLength = 25
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)
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)
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dt <- DT::formatRound(dt, "p_value", digits = 4)
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dt <- DT::formatPercentage(
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dt,
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c("total_ratio", "query_ratio"),
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digits = 1
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)
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})
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output$disgenet <- DT::renderDT({
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withProgress(
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message = "Querying DisGeNET",
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value = 0.0,
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{ # nolint
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setProgress(0.2)
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gene_names <- results_filtered()[, name]
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gene_names <- unique(gene_names[gene_names != ""])
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diseases <- suppressMessages(
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disgenet2r::disease_enrichment(gene_names)
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)
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data <- data.table(diseases@qresult)
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data <- data[, .(Description, Ratio, BgRatio, pvalue)]
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setorder(data, pvalue)
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dt <- DT::datatable(
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data,
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rownames = FALSE,
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colnames = c(
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"Disease",
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"Query ratio",
|
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"Total ratio",
|
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"p-value"
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),
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options = list(
|
||||
pageLength = 25
|
||||
)
|
||||
)
|
||||
|
||||
dt <- DT::formatRound(dt, "pvalue", digits = 4)
|
||||
|
||||
dt
|
||||
}
|
||||
)
|
||||
})
|
||||
}
|
||||
dt
|
||||
}
|
||||
)
|
||||
})
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue