在 R shiny 中使用猿 package 创建 phylog.netic 可视化

Question

I am creating a shiny web application to take newick input files from the user and then visualise the trees on the screen. I am trying to use the ape package to do this however I am getting stuck writing the server function in my shiny app. Would anyone be able to adjust my server function to be able to achieve the visualisation while also having some logic to detect the type of file that is being uploaded as well?

I have tried the following:

library(shiny)
library(ape)

ui <- navbarPage("Visualisation Toolbox", 
                 tabPanel("Phylogenic Trees",
                          fluidRow(
                            class = "inputs",
                            column(6, align = "center",
                                   h4("Select File Type:"),
                                   selectInput(inputId = "file_type", "", 
                                               choices = list("Newick" = "newick", 
                                                              "NEXUS" = "nexus",
                                                              "Phylip" = "phylip",
                                                              "RAxML" = "raxml"),
                                               selected = "newick")
                            ),
                            
                            column(6, align = "center",
                                   h4("Select Tree File:"),
                                   fileInput(inputId = "tree_file", "",
                                             buttonLabel = "Browse")
                            ), 
                            plotOutput('contents'),
                            )
                 ),
                 )

server <- function(input, output, session) {
  myPlot = reactiveVal()
  myData = reactive({
    input$tree_file
    myPlot(ape::read.tree(data))
    data
  })
  
  output$contents = renderPlot({
    myPlot()
  })
  }

shinyApp(ui = ui, server = server)

Answer 1

I don't understand fully what you mean by having some logic to detect file type. However the following example achieves visualization and plots conditionally on input$file_type . It may serve as a starting point.

library(shiny)
library(ape)
ui <- navbarPage("Visualisation Toolbox", 
                 tabPanel("Phylogenic Trees",
                          fluidRow(
                            class = "inputs",
                            column(6, align = "center",
                                   h4("Select File Type:"),
                                   selectInput(inputId = "file_type", "", 
                                               choices = list("Newick" = "newick", 
                                                              "NEXUS" = "nexus",
                                                              "Phylip" = "phylip",
                                                              "RAxML" = "raxml"),
                                               selected = "newick")
                            ),
                            column(6, align = "center",
                                   h4("Select Tree File:"),
                                   fileInput(inputId = "tree_file", "",
                                             buttonLabel = "Browse")
                            ), 
                            plotOutput(outputId  = 'contents'),
                            )
                 ),
                 )

server <- function(input, output, session) {
    output$contents <- renderPlot({
        file <- input$tree_file
        if (is.character(file$datapath)) {
            if (input$file_type %in% c("newick")) 
                plot(ape::read.tree(file$datapath))
        }})
}