Shiny 输出一个生成 pdf 文件本身的函数

Question

我正在尝试使用 Shiny 构建一个具有输出 pdf 文件功能的应用程序。具体来说，我尝试使用的函数是 msa 包中的 msaPrettyPrint 函数。它使用tools 包中的texi2pdf 函数来生成pdf 文件。 例如，如果您运行以下代码，您将在工作目录中生成一个名为“myFirstAlignment.pdf”的 pdf，其中包含氨基酸序列比对。

# source("http://www.bioconductor.org/biocLite.R")
# biocLite("msa")
library(msa)
mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa")
mySequences <- readAAStringSet(mySequenceFile)
myFirstAlignment <- msa(mySequences)
msaPrettyPrint(myFirstAlignment, output="pdf", showNames="left",showLogo="top",consensusColor="BlueRed", logoColors="accessible area", askForOverwrite=FALSE)

我想知道是否有办法使以下代码有效？我认为问题可能是因为输出已经是一个 pdf 文件。如果可能的话，我想在屏幕上看到 pdf 输出。如果在屏幕上看不到，pdf文件在哪里，我可以下载吗？

library(shiny)
runApp(list(
  #Load the exmaple from the msa package.
  mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa"),
  mySequences <- readAAStringSet(mySequenceFile),
  myFirstAlignment <- msa(mySequences),
  # A simple shiny app.
  # Is it possible to see the generated pdf file on screen?
  ui = fluidPage(plotOutput('plot')),
  server = function(input, output) {
    output$plot <- renderPlot(msaPrettyPrint(myFirstAlignment, output="pdf", showNames="left",showLogo="top",consensusColor="BlueRed", logoColors="accessible area", askForOverwrite=FALSE))
  }
))

要提一提的是，这段代码需要 LaTeX 才能工作。你需要 LaTeX 来运行这个例子。 非常感谢！

Answer 1

非常感谢 JackStat 和 Malanche 的帮助。下载结果如下！

library(shiny)
runApp(list(
   #Load the exmaple from the msa package.
   mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa"),
   mySequences <- readAAStringSet(mySequenceFile),
   myFirstAlignment <- msa(mySequences),
   # A simple shiny app.
   # Is it possible to see the generated pdf file on screen?
   ui = fluidPage(downloadButton('downloadPDF')),
   server = function(input, output) {
       output$downloadPDF = downloadHandler(
       filename = 'myreport.pdf',
       content = function(file) {
            msaPrettyPrint(
                myFirstAlignment
              , file = 'myreport.pdf'
              , output="pdf"
              , showNames="left"
              , showLogo="top"
              , consensusColor="BlueRed"
              , logoColors="accessible area"
              , askForOverwrite=FALSE)
       file.rename("myreport.pdf", file) # move pdf to file for downloading
       },
       contentType = 'application/pdf'
     )
  }
))

Answer 2

也许您可以使用msaPrettyPrint file 参数在本地存储pdf，然后使用此解决方案displaying a pdf from a local drive in shiny 在您的应用程序中放置一个pdf查看器。

Answer 3

我在运行您的示例时遇到了问题，但这应该可以工作

library(shiny)
runApp(list(
  #Load the exmaple from the msa package.
  mySequenceFile <- system.file("examples", "exampleAA.fasta", package="msa"),
  mySequences <- readAAStringSet(mySequenceFile),
  myFirstAlignment <- msa(mySequences),
  # A simple shiny app.
  # Is it possible to see the generated pdf file on screen?
  ui = fluidPage(downloadButton('downloadPDF')),
  server = function(input, output) {

    output$downloadPDF = downloadHandler(
      filename = 'myreport.pdf',

      content = function(file) {
        out = msaPrettyPrint(
              myFirstAlignment
              , file = 'myreport.pdf'
              , output="pdf"
              , showNames="left"
              , showLogo="top"
              , consensusColor="BlueRed"
              , logoColors="accessible area"
              , askForOverwrite=FALSE)
        file.rename(out, file) # move pdf to file for downloading
      },

      contentType = 'application/pdf'
    )

  }
))