Shiny-server, openxlsx plots not able to be inserted

Question

When running the following shiny app from the console with runApp(), it works as expected, displaying a plot and providing the ability to download an excel file with the plot embedded. Running the same app on shiny-server, yields the error

cannot open file 'Rplots.pdf'

Shiny Server v1.4.2.786
Node.js v0.10.40
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"

Ubuntu 14.04.4 LTS

library(shiny)
library(openxlsx)
library(magrittr)

# Define UI for application that draws a histogram
ui <- shinyUI(fluidPage(

   # Application title
   titlePanel("Old Faithful Geyser Data"),

   # Sidebar with a slider input for number of bins 
   sidebarLayout(
      sidebarPanel(
         sliderInput("bins",
                     "Number of bins:",
                     min = 1,
                     max = 50,
                     value = 30),
         downloadButton('specDataDownload',
                        label = "Download",
                        class = NULL)
      ),

      # Show a plot of the generated distribution
      mainPanel(
         plotOutput("distPlot")
      )
   )
))

# Define server logic required to draw a histogram
server <- shinyServer(function(input, output) {

   output$distPlot <- renderPlot({
      # generate bins based on input$bins from ui.R
      x    <- isolate({faithful[, 2] })
      bins <- seq(min(x), max(x), length.out = input$bins + 1)

      # draw the histogram with the specified number of bins
      hist(x, breaks = bins, col = 'darkgray', border = 'white')

   })
   output$specDataDownload <- downloadHandler(
       filename = function() {
           paste("ProcessedPlateAssay",
                 gsub("-|[[:space:]]|:",
                      "",
                      Sys.time()),
                 ".xlsx",
                 sep = "_")
       },
       content = function(con) {
           x    <- isolate({faithful[, 2] })
           bins <- seq(min(x), max(x), length.out = input$bins + 1)
           output <- createWorkbook()
           addWorksheet(
               output,
               "One")
           hist(
               x,
               breaks = bins,
               col = 'darkgray',
               border = 'white')
           insertPlot(
               output,
               sheet = 1,
               startRow = (1),
               startCol = 5,
               width = 6.5,
               height = 3,
               fileType = "png",
               units = "in",
               dpi = 600)

       saveWorkbook(
           wb = output,
           file = con
       )
       })
})

# Run the application 
shinyApp(ui = ui, server = server)

Ran into the same issue. Here's how we solved it: (1) use jpeg to open a (temporary) plot; (2) execute your plot command, (3) close the jpeg, use insertImage. — PMaier, Jul 21 '16 at 17:48
Hi, I ultimately solved that aspect as well but the underlying issue was that the shiny user on my server didn't have write permission to the folder (it was created as a git repository and pushed to the server). — bwbioinfo, Aug 26 '16 at 15:18

score 3 · Answer 1 · answered Oct 23 '18 at 10:56

I thought to provide a minimal example since I have struggled with the issue of openxlsx's insertPlot function not working inside shiny-server, probably due to permission issues with tempfile or dev.copy. The method that worked best for me was to use ggsave, since it handles resolution very neatly, and also has a scale parameter which allows resizing of the image elements making it more suitable for a presentation. I have also included a second method using the png function.

Below is a reproducible example, partly drawn from the answer by @sebkopf in Save plots made in a shiny app

library(shiny)
library(openxlsx)
library(ggplot2)

ui <- fluidPage(
  downloadLink("downloadExcel", "Excel Graph Download")
)

server <- function(input, output) {

  p1 <- qplot(mpg, data=mtcars, geom="density", fill=as.factor(gear), 
alpha=I(.5), main="Distribution of Gas Mileage")
  p2 <- qplot(age, circumference, data = Orange, geom = c("point", "line"), 
colour = Tree)

  output$downloadExcel <- downloadHandler(
    filename = "savePlot.xlsx",
    content = function(file){
      wb <- createWorkbook()

      addWorksheet(wb, "ggsave", gridLines = F)
      addWorksheet(wb, "png", gridLines = F)

      # Method 1: using ggsave

      ggsave("p1.png", plot = p1, scale = .6) # Scale parameter resizes the object making text more legible
      ggsave("p2.png", plot = p2, scale = .6)

      insertImage(wb, "ggsave", "p1.png", width = 5, height = 3.5)
      insertImage(wb, "ggsave", "p22.png", startCol = "J", width = 16, height = 10, units = "cm")

      # Method 2: using png function

      png("p11.png")
      print(p1)
      dev.off()

      insertImage(wb, "png", "p11.png", width = 5, height = 3.5)

      png("p22.png")
      print(p2)
      dev.off()

      insertImage(wb, "png", "p22.png", startCol = "J", width = 16, height = 10, units = "cm")

      saveWorkbook(wb, file, overwrite = T)

      unlink(c("p1", "p2", "p11", "p22")) # To remove the images from the server
    }
  )
}

shinyApp(ui, server)

And remember to check if shiny is the owner of the directory you are trying to write into: https://groups.google.com/forum/#!topic/shiny-discuss/srWETT6uL-I through `sudo chown shiny:shiny /var/shiny-server/www/shiny_test/work` — Joseph Kigotho, Nov 16 '18 at 15:28

Shiny-server, openxlsx plots not able to be inserted

1 Answers1