larry01 larry01 - 2 months ago 18
LaTeX Question

Shiny to output a function that generates a pdf file itself

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)


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))
}
))


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

Answer

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'
     )
  }
))
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