R/ShinyFunction.R

In GHLCLab/phexpo: Bidirectional enrichment analysis of phenotypes and chemicals

 ###########################################################################################################

#' Enrichment visualisation
#'
#' @param x Enrichment results tibble data frame.
#'
#' @return Shiny app.
#' @examples
#' \dontrun{
#' x <- perfFishTestChemSingle("Iodine")
#' visEnrich(x)}
#'
#'
#'
#'
#' @export
 visEnrich <- function(x){

if("HPO_Name" %in% colnames(x)) {
   shinyApp(
     ui = fluidPage(
       ###############################
       tags$style("
                  h1{
                  color:#008080;
                  }"),

       ################################################################
       #Ref to for selecting: https://shiny.rstudio.com/gallery/kmeans-example.html
       navbarPage(h1("Phexpo"),
           tabPanel(h3("Dataset"),
                    h4(tags$b("Table of Dataset")),
                    br(),
                    h4("Table 1. Enriched HPO Terms"),
                    div(dataTableOutput('table'),style="font-size:110%")), #Attribution: https://stackoverflow.com/questions/25069224/rstudio-shiny-renderdatatable-font-size

           tabPanel(h3("Bar chart"),
                  h4(tags$b("Phenotype Enrichment Bar chart")),
                  sidebarLayout(
                    sidebarPanel(
                    br(),
                    selectInput("valu","P-value selection",names(x[8:10]), selected = names(x[8])),
                    br()),

                    mainPanel(
                    numericInput("threshold",label = h4("Threshold Value"),0.05,min=0.000000000000000000000000005,max=0.5),
                    plotOutput("plot2")
                    )
                   )

         ))),

     server = function(input, output,session) {

       Dataset <- x
       Dataset_bar<- x %>%
         dplyr::mutate(logp = -log10(.data$p_value)) %>%
         dplyr::mutate(logb = -log10(.data$bonf)) %>%
         dplyr::mutate(logf = -log10(.data$FDR))


       ###### Data Table ##########
       output$table <- renderDataTable({Dataset})

       ######### Plots #########

         Dataset_3 <- reactive({
           if (input$valu == "p_value") {
           Dataset_bar$HPO_Name <- factor(Dataset$HPO_Name, levels = Dataset$HPO_Name[order(-Dataset$p_value)])
           Dataset_bar[,c("HPO_Name",input$valu)] %>% dplyr::filter(.[[2]] < input$threshold)
         } else if (input$valu == "bonf") {
           Dataset_bar$HPO_Name <- factor(Dataset$HPO_Name, levels = Dataset$HPO_Name[order(-Dataset$bonf)])
           Dataset_bar[,c("HPO_Name",input$valu)] %>% dplyr::filter(.[[2]] < input$threshold)
         } else {
           Dataset_bar$HPO_Name <- factor(Dataset$HPO_Name, levels = Dataset$HPO_Name[order(-Dataset$FDR)])
         Dataset_bar[,c("HPO_Name",input$valu)] %>% dplyr::filter(.[[2]] < input$threshold)
         }
         })


         output$plot2 <- renderPlot({
           Dataset_3() %>%
             ggplot2::ggplot(ggplot2::aes(x=.[[1]],y=.[[2]])) +
             ggplot2::geom_bar(stat="identity", fill="deepskyblue") +
             ggplot2::theme_bw() +
             ggplot2::theme(text = ggplot2::element_text(size=16)) +
             ggplot2::coord_flip() +
             ggplot2::ggtitle("Phenotype Enrichment") +
             ggplot2::xlab("HPO Term") +
             ggplot2::ylab(input$valu) })


     }
   )


} else if("Chemical_Name" %in% colnames(x)) {

  shinyApp(
    ui = fluidPage(

#########################################################################################
  tags$style("
             h1{
             color:#008080;
             }"),

  ################################################################
  navbarPage(h1("Phexpo"),
             tabPanel(h3("Dataset"),
                      h4(tags$b("Table of Dataset")),
                      br(),
                      h4("Table 1. Enriched Chemicals"),
                      div(dataTableOutput('table'),style="font-size:110%")),

             tabPanel(h3("Bar chart"),
                      h4(tags$b("Chemical Enrichment Bar chart")),
                      sidebarLayout(
                        sidebarPanel(
                          br(),
                          selectInput("valu","P-value selection",names(x[8:10]), selected = names(x[8])),
                          br()),

                        mainPanel(
                          numericInput("threshold",label = h4("Threshold Value"),0.05,min=0.000000000000000000000000005,max=0.5),
                          plotOutput("plot2")
                        )
                      )

             ))),

      server = function(input, output) {

        Dataset <- x
        Dataset_bar<- x %>%
          dplyr::mutate(logp = -log10(.data$p_value)) %>%
          dplyr::mutate(logb = -log10(.data$bonf)) %>%
          dplyr::mutate(logf = -log10(.data$FDR))


        ###### Data Table ##########
        output$table <- renderDataTable({Dataset})

        ######### Plots #########

        Dataset_3 <- reactive({
          if (input$valu == "p_value") {
            Dataset_bar$Chemical_Name   <- factor(Dataset$Chemical_Name, levels = Dataset$Chemical_Name[order(-Dataset$p_value)])
            Dataset_bar[,c("Chemical_Name",input$valu)] %>% dplyr::filter(.[[2]] < input$threshold)
          } else if (input$valu == "bonf") {
            Dataset_bar$Chemical_Name   <- factor(Dataset$Chemical_Name, levels = Dataset$Chemical_Name[order(-Dataset$bonf)])
            Dataset_bar[,c("Chemical_Name",input$valu)] %>% dplyr::filter(.[[2]] < input$threshold)
          } else {
            Dataset_bar$Chemical_Name   <- factor(Dataset$Chemical_Name, levels = Dataset$Chemical_Name[order(-Dataset$FDR)])
            Dataset_bar[,c("Chemical_Name",input$valu)] %>% dplyr::filter(.[[2]] < input$threshold)
          }
        })


        output$plot2 <- renderPlot({
          Dataset_3() %>%
            ggplot2::ggplot(ggplot2::aes(x=.[[1]],y=.[[2]])) +
            ggplot2::geom_bar(stat="identity", fill="deepskyblue") +
            ggplot2::theme_bw() +
            ggplot2::theme(text = ggplot2::element_text(size=16)) +
            ggplot2::coord_flip() +
            ggplot2::ggtitle("Chemical Enrichment") +
            ggplot2::xlab("Chemical") +
            ggplot2::ylab(input$valu) })

    }
  )


} else {print("Please provide the results of your enrichment analysis.")}




 }