geposanui/R/gsea.R

#' Create a GSEA page.
#' @noRd
gsea_ui <- function(id) {
  verticalLayout(
    filters_ui(NS(id, "filters")),
    div(
      class = "flow-layout",
      actionButton(
        NS(id, "gsea_run"),
        "Update analysis",
        class = "btn-primary"
      ),
      a(
        "Powered by g:Profiler",
        href = "https://biit.cs.ut.ee/gprofiler/gost",
        target = "_blank",
        style = "margin-left: 16px"
      )
    ),
    tabsetPanel(
      id = NS(id, "results"),
      type = "hidden",
      tabPanelBody(
        "some",
        div(
          style = "margin-top: 16px",
          plotly::plotlyOutput(NS(id, "plot")),
        ),
        div(
          style = "margin-top: 16px",
          DT::DTOutput(NS(id, "details"))
        )
      ),
      tabPanelBody(
        "none",
        div(
          style = "margin-top: 32px",
          h5("No results"),
          div(
           "The enrichment analysis using g:Profiler yielded no results. ",
           "You can change the parameters of the ranking and the filter ",
           "criteria. Click the \"Update analysis\" button to rerun the ",
           "analysis."
          )
        )
      )
    )
  )
}

#' Create a server for the comparison editor.
#'
#' @param id ID for namespacing the inputs and outputs.
#' @param ranking The ranking to be analyzed.
#'
#' @noRd
gsea_server <- function(id, ranking) {
  moduleServer(id, function(input, output, session) {
    ranking_filtered <- filters_server("filters", ranking)

    gsea_analysis <- reactive({
      withProgress(
        message = "Querying g:Profiler",
        value = 0.0,
        { # nolint
          setProgress(0.2)
          gprofiler2::gost(
            ranking_filtered()$gene,
            custom_bg = ranking()$gene,
            domain_scope = "custom_annotated"
          )
        }
      )
    }) |>
      bindCache(ranking_filtered()) |>
      bindEvent(input$gsea_run, ignoreNULL = FALSE)

    observe({
      updateTabsetPanel(
        session,
        "results",
        selected = if (!is.null(gsea_analysis()$result)) {
          "some"
        } else {
          "none"
        }
      )
    })

    output$plot <- plotly::renderPlotly({
      if (!is.null(gsea_analysis()$result)) {
        gprofiler2::gostplot(
          gsea_analysis(),
          capped = FALSE,
          interactive = TRUE
        )
      } else {
        plotly::plotly_empty()
      }
    })

    output$details <- DT::renderDT({
      if (!is.null(gsea_analysis()$result)) {
        data <- data.table(gsea_analysis()$result)
        setorder(data, p_value)

        data[, total_ratio := term_size / effective_domain_size]
        data[, query_ratio := intersection_size / query_size]
        data[, increase := (query_ratio - total_ratio) / total_ratio]

        data <- data[, .(
          source,
          term_name,
          total_ratio,
          query_ratio,
          increase,
          p_value
        )]

        DT::datatable(
          data,
          rownames = FALSE,
          colnames = c(
            "Source",
            "Term",
            "Total ratio",
            "Query ratio",
            "Increase",
            "p-value"
          ),
          options = list(
            pageLength = 25
          )
        ) |>
          DT::formatRound("p_value", digits = 4) |>
          DT::formatPercentage(
            c("total_ratio", "query_ratio", "increase"),
            digits = 2
          )
      } else {
        DT::datatable(data.table())
      }
    })
  })
}