inst/shinyapp/modules/combo-single-gene-pan-cancer-analysis.R

In UCSCXenaShiny: Interactive Analysis of UCSC Xena Data

ui.combo.sg.pancan.analysis <- function(id) {
  ns <- NS(id)
  fluidPage(
    titlePanel("Combo: Single Gene Pan-Cancer Analysis"),
    sidebarLayout(
      sidebarPanel = sidebarPanel(
        ## input gene
        shinyWidgets::searchInput(
          inputId = ns("Pancan_search"),
          label = NULL,
          btnSearch = icon("search"),
          btnReset = icon("remove"),
          placeholder = "Enter a gene symbol to show its pan-can distribution, e.g. TP53",
          width = "100%"
        ),
        selectInput(
          inputId = ns("immune_sig"), "Select the immune signature source", selected = "Cibersort",
          choices = c("Yasin", "Wolf", "Attractors", "ICR", "c7atoms", "Bindea", "Cibersort")
        ),
        width = 3
      ),
      mainPanel = mainPanel(
        ## pancan distribution
        plotOutput(ns("gene_pancan_dist")),
        ## uni-cox survival analysis
        plotOutput(ns("unicox_gene_tree")),
        ## heatmap: correlation between gene and immune signatures
        plotOutput(ns("hm_gene_immune_cor")),
        width = 9
      )
    )
  )
}

server.combo.sg.pancan.analysis <- function(input, output, session) {
  observeEvent(input$Pancan_search, {
    if (nchar(input$Pancan_search) >= 1) {
      output$gene_pancan_dist <- renderPlot({
        vis_toil_TvsN(
          Gene = input$Pancan_search,
          Mode = "Boxplot",
          Method = "wilcox.test",
          Show.P.value = TRUE,
          Show.P.label = TRUE,
          include.Tumor.only = TRUE
        )
      })

      output$unicox_gene_tree <- renderPlot({
        vis_unicox_tree(
          Gene = input$Pancan_search
        )
      })

      output$hm_gene_immune_cor <- renderPlot({
        vis_gene_immune_cor(
          Gene = input$Pancan_search,
          Immune_sig_type = input$immune_sig
        )
      })
    }
  })
}