在 r 闪亮的模块中使用反应值

Question

你好 RShiny 社区 -

我仍然有点难以思考如何在模块之间传递反应值。下面，我有三个模块以及顶级服务器和 ui 功能。 三个模块会这样做（理论上） 1）uploadTree 模块将允许用户输入和读取系统发育树文件； 2) paramsTree 模块将是多个树可视化输入，用户可以选择并在从 uploadTree 模块导入的树上更改； 3) displayTree 模块将是显示树并根据用户输入（即对齐 = T 或 F）调整可视化的模块。

但是，我仍然很难让它工作 - 最终可能是因为我仍然不清楚使模块相互通信的正确方法。就目前而言，此代码不允许树显示并给出错误'找不到函数'align''

建议....

下面是一个在 align = T 中硬编码的例子：

library(shiny)
library(ggtree)

#top-level ui
ui <- 
    fluidPage(
      h1("phylogeny"),
      sidebarPanel(
        mod_uploadTree_ui("uploadTree_ui_1")),
        #mod_paramsTree_ui("paramsTree_ui_1")), #commented out as this is not working 
      mainPanel(mod_displayTree_ui("displayTree_ui_1"))
    )

#top-level server
server <- function(input, output,session) {

  treeDisplay <- callModule(mod_uploadTree_server, "uploadTree_ui_1")
  #params <- callModule(mod_paramsTree_server, "paramsTree_ui_1") #commented out as this is not working. 
  callModule(mod_displayTree_server, "displayTree_ui_1", treeDisplay)
}

#uploadTree module - This module will use the read.newick function to read in a phylogenetic tree
mod_uploadTree_ui <- function(id){
  ns <- NS(id)
  tagList(
    fileInput(ns("treefile"), label="Upload a newick file, please"))
}


mod_uploadTree_server <- function(input, output, session){
  ns <- session$ns

  treeFile <- reactive({
    req(input$treefile)
    treeio::read.newick(input$treefile$datapath)
  })
}

  #paramsTree module - This module *should* include multiple tree display parameters that can be selected by the user. Here, only one parameter is included for a smaller example. But I am unable to add this without an error occurring. 
  mod_paramsTree_ui <- function(id){
    ns <- NS(id)
    tagList(
      checkboxInput(ns("alignTips"), "Align tip labels", TRUE)
    )
  }

  mod_paramsTree_server <- function(input, output, session){
    ns <- session$ns

    observe({
      align = reactive(input$alignTips)
    })
  }

  #displayTree module - This module will plot the tree and will change the tree viz based on user inputs from param module 
  mod_displayTree_ui <- function(id, label = "Display Tree"){
    ns <- NS(id)
    tagList(
      label,
      plotOutput(ns("treeDisplay"))
    )
  }

  mod_displayTree_server <- function(input, output, session, treeFile, align){
    ns <- session$ns

    make_tree <- reactive({
      ggplot2::ggplot(treeFile()) + ggtree::geom_tree() + ggtree::geom_tiplab(align = T) #hardcoded align = T instead of based on user input
    })

    output$treeDisplay <- renderPlot({
      make_tree()
    })
  }

shinyApp(ui, server)

根据 bretauv 的建议，这里是读取系统发育并绘制系统发育与提示对齐的代码。

library(ggplot2)
library(treeio)
library(ggtree)

tree <- treeio::read.newick("1509MLJF6-1.dnd")
make_tree <- ggplot2::ggplot(tree) + ggtree::geom_tree() + ggtree::geom_tiplab(align = T)
make_tree

如果需要，系统发育树位于here

Answer 1

您的每个服务器函数都必须返回一个reactive（或reactiveValues 或reactiveVal），例如：

mod_uploadTree_server <- function(input, output, session){
  ns <- session$ns

  treeFile <- reactive({
    req(input$treefile)
    treeio::read.newick(input$treefile$datapath)
  })

return(treeFile)
}