R/ici_neoantigen_classes_server.R

In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)

ici_neoantigen_classes_server <- function(
    id,
    cohort_obj,
    count_df,
    dataset_displays,
    legend_plot
) {
  shiny::moduleServer(
    id,
    function(input, output, session) {

      ns <- session$ns

      cohort_count <- shiny::reactive({
        cohort_obj()$sample_tbl %>%
          dplyr::inner_join(count_df, by = c("sample_name" = "sample")) %>%
          dplyr::mutate(ERROR = NA) %>%
          dplyr::group_by(dataset_name, group_name, feature_name) %>%
          dplyr::mutate(y = sum(feature_value)) %>%
          dplyr::mutate(text = paste("Neoantigen class: ", feature_name, "\n Group: ", group_name, "\n Count: ", y)) %>%
          dplyr::select(dataset_name, group_name, feature_name, y, ERROR, text) %>%
          dplyr::distinct()
      })

      all_plots <- shiny::reactive({
        shiny::req(cohort_count())
        shiny::validate(shiny::need(nrow(cohort_count())>0, "There is no neoantigen data for the selected dataset(s)"))

        purrr::map(cohort_obj()$dataset_names, function(x){
          dataset_df <-  cohort_count() %>%
            dplyr::filter(dataset_name == x)

          if(nrow(dataset_df)>0){
            dataset_df %>%
              create_barplot(
                .,
                x_col = "feature_name",
                y_col = "y",
                error_col = "ERROR",
                key_col = NA,
                color_col = "group_name",
                label_col = "text",
                title = "",
                source_name = "neo_class",
                bar_colors = unique(cohort_obj()$plot_colors),
                showlegend = FALSE
              ) %>%
              add_title_subplot_plotly(unname(dataset_displays()[x]))
          }
        }) %>% Filter(Negate(is.null),.)
      })

      output$classes_plot <- shiny::renderUI({
        shiny::req(all_plots())
        n_rows = (length(all_plots())+2)%/%3
        box_height = paste0(n_rows*400, "px")

        plotly::plotlyOutput(ns("neoantigen_classes_plot"), height = box_height)
      })

      output$legend <-  DT:: renderDT({
        shiny::req(cohort_count())
        shiny::validate(shiny::need(nrow(cohort_count())>0, ""))
        legend_plot()})

      output$neoantigen_classes_plot <- plotly::renderPlotly({
        shiny::req(all_plots())
        plotly::subplot(all_plots(), nrows = (length(all_plots())+2)%/%3, margin = c(0.02, 0.02, 0.1, 0.1))
      })

      observeEvent(input$method_link,{
        shiny::showModal(modalDialog(
          title = "Method",
          includeMarkdown("inst/markdown/methods/neoantigen-classes.markdown"),
          easyClose = TRUE,
          footer = NULL
        ))
      })
    }
  )
}