Using an app to automate a firm specific shiny document, ggplotly and dataTable do not work

Question

I am writing a shiny app that I want to deploy that produces a "rmarkdown document" for a given firm "on the fly". My Rmarkdown template takes Ticker as a parameter, filters the data, produces a table using kableExtra, a table using DT, a plot using ggplot, and a plot using ggplotly. Everything works fine when I run the template. When I embed the template into a shiny app following this approach:

https://davidruvolo51.github.io/shinytutorials/tutorials/rmarkdown-shiny/#:~:text=Rmarkdown%20is%20perfect%20for%20shiny,server%20into%20a%20Rmd%20template.

The kableExtra and the ggplot work, bu the DT and ggplotly are simply "not there". Can someone help? Suppose I would very much like to use both DT and ggplotly in this context.

Here is my "global.R" file:

tickers = c("AAPL","ATVI","AMZN","AON","AXP","BAC","BK","BYDDF",
                  "C","CE","CHTR","CVX","DEO","DVA","FND","FWONK","GL","GM","HPQ",
                  "ITOCF","JEF","JNJ","KHC","KO","KR","LILA","LILAK","LPX","LSXMA","LSXMK",
                  "MA","MCK","MCO","MDLZ","MKL","MMC","NU","OXY","PARA","PG",
                  "RH","SNOW","STNE","TMUS","TSM","UPS","USB","V","VRSN")

df  <- data.frame(tickers = rep(tickers,each=10),year = rep(11:20,length(tickers)), returns = rnorm(10*length(tickers)) )

library(dplyr)
library(shiny)
library(kableExtra)
library(ggplot2)
library(DT)
library(plotly)

Here is my template which is an .Rmd file. I marked the start and end of the code blocks with #``` so that the whole thing would look like code in this context. To get it to run you will need to delete the #.

---
title: "Test running an Rmarkdown Report via a Shiny App"
output: html_document
runtime: shiny


params: 
    ticker: MCO
---
 
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE, eval=TRUE, message=FALSE, warning=FALSE)
        ticker007 = params$ticker

```

You have selected `r params$ticker`

print the firm

```{r}
filtered = df[df$ticker==ticker007,]
print(filtered)
```

# Test kableExtra:

```{r,fig.fig.align='center'}
kableExtra::kable(filtered) %>% kable_styling()
```


# Test DataTable:
```{r}
DT::datatable(filtered,filter = "none", options = list(pageLength=20,dom = "tip", bFilter = 0, bSort = 0, bProcessing = 0, bPaginate = 0, bInfo = 0,rownames=F),class=list(class="row-border")) %>%  DT::formatStyle(names(filtered),backgroundColor = "white")  
```


# Test ggplot:

```{r}
plot1 <- ggplot(filtered,aes(x=year,y=returns)) + geom_path()
plot1
```

# Test ggplotly:

```{r}

 ggplotly(plot1)
```

And this is my app:

source('global.R')

# Define UI for application that draws a histogram
ui <- fluidPage(
  selectInput(
    'ticker', 'Select ticker',
    choices = tickers ),
  htmlOutput('report')
)

server <- function(input, output) {
  output$report <- renderUI({
    includeHTML(
      rmarkdown::render(
        'testTemplate.Rmd',
        params = list(ticker = input$ticker)
      )
    )
  })
}

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

Answer 1

Not a good answer but too long for a comment.

The problem is that your Shiny app does not include the necessary JavaScript files (the plotly library for example).

If you add a DT table and a plotly chart in your app, then this will work:

source("global.R")
# Define UI for application that draws a histogram
ui <- fluidPage(
  
  DTOutput("dtable"),
  plotlyOutput("plotly"),

  br(),
  tags$hr(),
  br(),
  
  selectInput(
    'ticker', 'Select ticker',
    choices = tickers ),
  htmlOutput('report')
)

server <- function(input, output) {
  output$dtable <- renderDT({
    datatable(iris[1:5, ])
  })
  
  output$plotly <- renderPlotly({
    p <- ggplot(mtcars, aes(wt, mpg))
    p + geom_point()
  })
  
  output$report <- renderUI({
    includeHTML(
      rmarkdown::render(
        'testTemplate.Rmd',
        params = list(ticker = input$ticker)
      )
    )
  })
}

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

But you also have to use html_fragment as output type of the Rmd, otherwise jQuery is included two times and that's bad:

---
title: "Test running an Rmarkdown Report via a Shiny App"
output: html_fragment
runtime: static
params: 
    ticker: MCO
---

Of course you don't want to add a DT table and a plotly chart in your app. One solution is to hide them (with the CSS display: none). Or maybe you can render an empty DT table and an empty plotly chart...

Another, better solution would be to include the JavaScript libraries with htmltools::htmlDependency.

Answer 2

I think You may omit the shiny application. In Your markdown You use shiny runtime, so what You need is to put the select input directly into the rmarkdown file and then use shiny::render* functions to render the outputs:

    ---
    title: "Test running an Rmarkdown Report via a Shiny App"
    output: html_document
    runtime: shiny
    ---
      
    ```{r setup, include=FALSE}
    knitr::opts_chunk$set(echo = FALSE, eval=TRUE, message=FALSE, warning=FALSE)
    ```
    
    ```{r}
    library(shiny)
    library(DT)
    library(ggplot2)
    library(plotly)
    ```
    
    
    ```{r}
    tickers = c("AAPL","ATVI","AMZN","AON","AXP","BAC","BK","BYDDF",
                      "C","CE","CHTR","CVX","DEO","DVA","FND","FWONK","GL","GM","HPQ",
                      "ITOCF","JEF","JNJ","KHC","KO","KR","LILA","LILAK","LPX","LSXMA","LSXMK",
                      "MA","MCK","MCO","MDLZ","MKL","MMC","NU","OXY","PARA","PG",
                      "RH","SNOW","STNE","TMUS","TSM","UPS","USB","V","VRSN")
    
    df  <- data.frame(
      tickers = rep(tickers,each=10),
      year = rep(11:20, length(tickers)),
      returns = rnorm(10*length(tickers))
    )
    
    shiny::selectInput(
      'ticker', 'Select ticker',
      choices = tickers )
    ```
    
    
    ```{r}
    filtered_data <- eventReactive(input$ticker, {
      filtered = df[df$ticker == input$ticker,]
    })
    ```
    
    ```{r}
    DT::renderDataTable({
      DT::datatable(filtered_data())
    })
    
    ```
    
    ```{r}
    renderPlotly({
      plot1 <- ggplot(
        filtered_data(),
        aes(x=year,y=returns)
    ) + geom_path()
      
      plotly::ggplotly(plot1)  
    })
    ```

Please, see this reference https://bookdown.org/yihui/rmarkdown/interactive-documents.html#intro-shiny

I know that this is not exactly what You were asking for, but it's hard for me to see the reason why You're trying to combine shiny and rmarkdown this way. Maybe with a little bit more context it will be clear.