I am wondering if it is possible to pass a plot object to Rmarkdown document when generating a downloadable report using shiny?

For instance,I have a P2 plotly object, I want to pass it to Rmarkdown document.

I know I can put the code in Rmarkdown and generate the plot, but I don't to do it here

output$Plot <- plotly::renderPlotly({
p <- ggplot(data=iris, aes(x = Sepal.Length, y = Sepal.Width))  
      geom_point(aes(color=Species, shape=Species))  
      labs(title = "Iris sepal width vs length")
P2 <- ggplotly(p)
})

How can I pass it in downloadHandler() ?

output$report <- downloadHandler(

 params <- list(myPlot = p2)

)

CodePudding user response：

Lets have files doc.Rmd:

---
title: "Untitled"
author: "danlooo"
date: "2/22/2022"
params:
  plot:
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Plot

```{r}
params$plot
```

And another file app.R in the same directory:

library(shiny)
library(plotly)
library(tidyverse)
library(rmarkdown)

ui <- fluidPage(
  plotlyOutput("plot"),
  downloadButton("download")
)

server <- function(input, output, session) {
  plot <- reactive({
    p <- ggplot(data = iris, aes(x = Sepal.Length, y = Sepal.Width))  
      geom_point(aes(color = Species, shape = Species))  
      labs(title = "Iris sepal width vs length")

    ggplotly(p)
  })

  output$plot <- renderPlotly(plot())

  output$download <- downloadHandler(
    filename = "report.html",
    content = function(file) {
      render(input = "doc.Rmd", output_dir = dirname(file), 
       output_file = basename(file), params = list(plot = plot()))
    }
  )
}


shinyApp(ui, server)

Then you can downlaod the report after clicking the button.

CodePudding user response：

You can wrap the resulting plotly object in reactive or reactiveVal to pass it to the output and the downloadHandler:

library(shiny)
library(plotly)

writeLines(con = "report.Rmd", text = "---
title: 'Plotly report'
output: html_document
params:
  plotly_object: NA
---

```{r plotlyout, echo=FALSE, message=FALSE, out.width='100%'}
params$plotly_object
```")

ui = fluidPage(
  plotlyOutput("Plot"),
  downloadButton("report_button", "Generate report")
)

server = function(input, output, session) {
  irisPlot <- reactive({
    p <- ggplot(data=iris, aes(x = Sepal.Length, y = Sepal.Width))  
      geom_point(aes(color=Species, shape=Species))  
      labs(title = "Iris sepal width vs length")
    ggplotly(p)
  })

  output$Plot <- plotly::renderPlotly({
    irisPlot()
  })

  output$report_button <- downloadHandler(
    filename = "report.html",
    content = function(file) {
      tempReport <- tempfile(fileext = ".Rmd") # make sure to avoid conflicts with other shiny sessions if more params are used
      file.copy("report.Rmd", tempReport, overwrite = TRUE)
      rmarkdown::render(tempReport, output_format = "html_document", output_file = file, output_options = list(self_contained = TRUE),
                        params = list(plotly_object = irisPlot())
      )
    }
  )
}

shinyApp(ui, server)

Another approach is using htmlwidgets::saveWidget (If you only need the html plot):

library(shiny)
library(plotly)

ui = fluidPage(
  plotlyOutput("Plot"),
  downloadButton("report_button", "Generate report") 
)

server = function(input, output, session) {
  irisPlot <- reactive({
    p <- ggplot(data=iris, aes(x = Sepal.Length, y = Sepal.Width))  
      geom_point(aes(color=Species, shape=Species))  
      labs(title = "Iris sepal width vs length")
    ggplotly(p)
  })
  
  output$Plot <- plotly::renderPlotly({
    irisPlot()
  })
  
  output$report_button <- downloadHandler(
    filename = "report.html",
    content = function(file) {
      htmlwidgets::saveWidget(widget = partial_bundle(irisPlot()), file = file, selfcontained = TRUE)
    }
  )
}

shinyApp(ui, server)