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以下代码生成一个 GUI，用户可以在其中输入文件路径。代码预处理这些文件路径并保护结果。这个想法是将这些输入传递给 Rmarkdown 的渲染函数，并在第一次按下操作按钮时将这些值发送到渲染函数，以便渲染另一个使用这些值的 Rmarkdown 文件。这就是它在理论上的工作原理，实际上第一次按下按钮会导致渲染发生，但实际上没有任何参数是与第一次按下按钮一起发送的。但是，按下第二个按钮，一切正常。谁能看到我的代码中的缺陷，即阻止第一个按钮按我想要的方式运行？

我试着环顾四周，看看其他人是否已经弄清楚了，老实说，我认为我发现的只是也许我使用了隔离（）？抱歉，我对 R 闪亮很陌生。

GUIforRmarkdowngeneration

标题：“为数据生成 Rmarkdown 报告”运行时：闪亮

输出：html_notebook

#setwd("/home/alan/Desktop/wts/filestosaveandcarryover/tiamatfiles")
knitr::opts_chunk$set(echo=TRUE)
library(reticulate) # <- only needed to run python
#use_python("/Users/dyarmosh/anaconda3/bin/python")

library(shinyFiles)
library(glue)
library(stringr)

ui <- fluidPage(
   sidebarLayout(
    sidebarPanel(
  shinyFilesButton("Btn_GetFile", "Choose forward fastq" ,
                   title = "Please select a file:", multiple = FALSE,
                   buttonType = "default"),
  br(),
  selectInput("Selected_Panel", "Select Panel", choices = c("bacillus","burkholderia","yersinia")),
  br(),
  # #submitButton("Begin Analysis") - fix this no select item from file system
  actionButton("Start", "Begin Analysis")
  ),
  mainPanel(
      br(),
      textOutput("fwdftext"),
      br(),
      textOutput("revftext"),
      br(),br(),
      textOutput("paneltext"),
      br(),br(),
      textOutput("completion")

    ))
)

rvs <- reactiveValues() #renamed to rvs
server <- function(input,output,session){

  volumes = getVolumes()
  observe({  
    shinyFileChoose(input, "Btn_GetFile", roots = volumes, session = session)

    req(input$Btn_GetFile)
    req(input$Selected_Panel)
    req(input$Start)

    fwd_selected <- parseFilePaths(volumes, input$Btn_GetFile)

    rvs$fwdfastq <- as.character(fwd_selected$datapath)
    if (str_detect(rvs$fwdfastq,"R1")){rvs$revfastq <- str_replace(rvs$fwdfastq,"R1","R2")}
    if (str_detect(rvs$fwdfastq,"R2")){rvs$revfastq <- str_replace(rvs$fwdfastq,"R2","R1")}
    class_selected <- parseFilePaths(volumes, input$ClassifierFile)
    kmer_selected <- parseFilePaths(volumes, input$StoredKmerFile)
    rvs$panopt <- as.character(input$Selected_Panel)
    rvs$start <- input$Start
    output$fwdftext <- renderText({paste("Entered Forward File:", rvs$fwdfastq)})
    output$revftext <- renderText({paste("Matched Reverse File:", rvs$revfastq)})
    output$paneltext <- renderText({paste("Entered Panel:", rvs$panopt)})
  })
  observeEvent(input$Start, {
        print(paste(rvs$panopt,rvs$fwdfastq,rvs$revfastq, rvs$class,rvs$kmer))
            rmarkdown::render("testinput.Rmd", 
                      params = list(
                        panelname =  rvs$panopt, 
                        r1filename = rvs$fwdfastq, 
                        r2filename =  rvs$revfastq, 
                        classifier = rvs$class, 
                        kmer = rvs$kmer
                        ), 
                      output_file = paste0("AmpSeqClass_Report_",strsplit(basename(toString(rvs$fwdfastq)),"[.]")[[1]][1],"_",str_replace(c(Sys.time())," ","_"),".html"))

        output$completion <- renderText({paste("Rmarkdown Document render is complete at ",toString(Sys.time()))})
  })

}
observe({
  req(rvs$fwdfastq)
  req(rvs$revfastq)
  req(rvs$panopt)
  req(rvs$start)
})



shinyApp(ui = ui, server = server)

testinputfile.Rmd

标题：执行内容输出：html_document：参数：r1filename：标签：“转发：”值：BurkP-130611_S12_100_L001_R1_001.fastq r2filename：标签：“反向：”值：BurkP-130611_S12_100_L001_R2_001.fastq 面板名称：标签：“AP：”值：芽孢杆菌输入：选择选项：[芽孢杆菌、伯克霍尔德氏菌、耶尔森氏菌]

setwd("/home/alan/Desktop/wts/filestosaveandcarryover/tiamatfiles")
knitr::opts_chunk$set(echo=TRUE)
library(reticulate) # <- only needed to run python
#use_python("/Users/dyarmosh/anaconda3/bin/python")

print(params)

基本上，如果您可以在第一次单击操作按钮时正确生成 rmarkdown，并且传递的参数都不是 NULL，那就是解决方案

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