Rmarkdown in Shiny Application

RMarkdown in Shiny Application

I think knitting it and rendering a UI should work.

library(shiny)
library(knitr)

ui <- shinyUI(
    fluidPage(
        uiOutput('markdown')
  )
)
server <- function(input, output) {
    output$markdown <- renderUI({
        HTML(markdown::markdownToHTML(knit('RMarkdownFile.rmd', quiet = TRUE)))
    })
}

shinyApp(ui, server)

Use R Markdown .docx template in shiny app

Keep your rmarkdown and word template in app folder.

In your downloadhandler:

        output$your_output <- downloadHandler(
            filename = function() {
                'output_title.docx'
            },
            content = function(file) {
                tempReport <- file.path(temp_folder, 
                       "rmarkdown_template.Rmd")
                tempTemplate <- file.path(temp_folder, "template.docx")
                file.copy("rmarkdown_template.Rmd", tempReport, overwrite = TRUE)
                file.copy("template.docx", tempTemplate, overwrite = TRUE)

                # Params
                
                )
                rmarkdown::render(tempReport, output_file = file, output_format = 'word_document',
                                  params = params,
                                  envir = new.env(parent = globalenv())
                )
            }
        )

Then in your yaml:

output: 
  word_document:
    reference_docx: template.docx

Passing a dataframe as a parameter from Shiny app to RMarkdown

There are several issues with your code. I'll go over them one by one

Invalid parameter in downloadHandler()

You are passing an object of class reactive to the contentType parameter of downloadHandler().

downloadHandler(
  reactive(file <- input$file1),     ## <--- here
  filename = "report.doc",
  content = function(file) {
    # ...
  }
)

It seems that this messes up the whole logic of downloadHandler() and leads to "server error" messages on the client side with no errors or warnings from shiny.

This line needs to be removed in order to download files successfully

Reference the Rmd-parameter correctly

When you want to access the parameter from the Rmd report, you will need to use params$report.data. Just using report.data will lead to the following error: object 'report.data' not found.

---
output: word_document
params:
  report.data: NULL
---

```{r}
report.data <- params$report.data
# ...
```

Fix the path to the generated file

You are knitting the Rmd inside the temporary directory, which is generally a good idea. However, getting the paths right is not always that easy. In your case, I used the following

rendered_report <- rmarkdown::render(
  tempReport, output_file = "wordreport.doc",
  params = params,
  envir = new.env(parent = globalenv())
)
file.copy(rendered_report, file)

The reason your version didn't work is that the generated report is created inside the temporary directory alogside tmpReport. See the reference documentation of ?rmarkdown::render for more details.

I used the return value of rmarkdown::render() instead which holds an absolute path to the generated file. This is less error prone and especially useful if you do not know the file extension of the generated file in advance

Use read.csv to convert the uploaded file into a data.frame

Shiny doesn't automatically convert uploaded csv files into dataframes. You need to define a parsing logic to do that.

params <- list(report.data = read.csv(input$file1$datapath))

One final word

Try to get more organized with your coding projects and limit the scope of future SO questions to one issue at a time. Creating "minimal reproducible examples" might seem tedious at first, but there are several advantages in doing that

• Other people can read the questions and answers and reuse them in their own projects easily without dissecting a wall of code
• It is much easier to answer those questions. With questions like this, the SO community usually only provides comments because answering them properly requires a lot of effort
• Minimizing and isolating problems is a skill that will help you to figure out issues in your future coding projects much more easily

My shiny app does not render R code in markdown

I think the problem will be, that you are copying your prot.Rmd to a tempfile with fileext = ".html" - it should be ".Rmd".

Please try the following:

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

    # Application title
    titlePanel("Knit"),

    downloadButton("prot", "Render file")
)

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

    output$prot <- downloadHandler(
      
        # For PDF output, change this to "report.pdf"
        filename = "prot.html",
        
        content = function(file) {
            
            report_path <- tempfile(fileext = ".Rmd")
            file.copy("prot.Rmd", report_path, overwrite = TRUE)
            
            
            rmarkdown::render(report_path,
                              output_file = file)
            
        }
    )
}

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

How to pass a reactive plot generated in Shiny to Rmarkdown to generate dynamic reports

Basically your question already included all the building blocks. I only updated the report template to include the code to plot the radar chart. As a parameter I decided to pass the filtered dataset. In the server I only adjusted the specs for the params:

server <- function(input, output) {
  output$plot1 <- renderChartJSRadar({
    chartJSRadar(skills[, c("Label", input$selectedPeople)], 
                 maxScale = 10, showToolTipLabel=TRUE) 
  })
  
  output$report <- downloadHandler(
    filename = "report.html",
    content = function(file) {
      tempReport <- file.path(tempdir(), "report.Rmd")
      file.copy("report.Rmd", tempReport, overwrite = TRUE)
      
      params <- list(scores = skills[, c("Label", input$selectedPeople)])

      rmarkdown::render(tempReport, output_file = file,
                        params = params,
                        envir = new.env(parent = globalenv())
      )
    }
  )
}

Report.Rmd

---
title: "Dynamic report"
output: html_document
params:
  scores: NA
---

```{r}
chartJSRadar(params$scores, maxScale = 10, showToolTipLabel=TRUE)
```

---

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