闪亮输出一个函数，该函数本身会生成pdf文件

问题描述

我正在尝试使用Shiny构建具有输出pdf文件的功能的应用程序.具体来说，我要使用的函数是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，如果运行以下代码，您将在工作目录中生成一个名为"myFirstAlignment.pdf"的pdf文件，其中包含氨基酸序列比对.

I am trying to use Shiny to build an app with a function that output a pdf file. Specifically, the function I am trying to use is the msaPrettyPrint function from the msa package. It uses the texi2pdf function from the tools package to generate a pdf file.For example, if you run the following code, you will generate a pdf called "myFirstAlignment.pdf" with an amino acid sequence alignment in your working directory.

# 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)

我想知道是否有一种方法可以使以下代码正常工作?我认为问题可能是因为输出已经是pdf文件.如果可能的话，我想在屏幕上看到pdf输出.如果无法在屏幕上看到它，则pdf文件在哪里，我可以下载它吗?

I was wondering if there is a way to make the following code works? I think the problem might be because the output is already a pdf file. I want to see the pdf output on screen if possible. If not possible to see it on screen, where is the pdf file and if I can download it?

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))
  }
))

要提到的一件事是，此代码需要LaTeX才能起作用.您将需要LaTeX来运行示例.非常感谢！

One thing to mention is that this code needs LaTeX to work. You would need LaTeX to run the example.Thanks a lot!

推荐答案

非常感谢JackStat和Malanche的帮助.以下内容可用于下载结果！

Thanks so much for the help from JackStat and Malanche. The following works for downloading the result!

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'
     )
  }
))

这篇关于闪亮输出一个函数，该函数本身会生成pdf文件的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持！