How to add table of contents in rmarkdown html Shiny app - html

Question

Based on this link I tried to include a table of contents in an HTML rmarkdown output. This works fine if I just knit it in RStudio, but when I try the same in Shiny, the table of contents doesn't show up. Am I doing something wrong or is this simply not possible? I also tried some custom css but that also doesn't seem to work. I need this because my users need to set some inputs and download an interactive document themselves with a toc. Please find an example below.
server.r
library(shiny)
library(rmarkdown)
library(htmltools)
library(knitr)
shinyServer(function(input, output) {
output$distPlot <- renderPlot({
# generate bins based on input$bins from ui.R
x <- faithful[, 2]
bins <- seq(min(x), max(x), length.out = input$bins + 1)
# draw the histogram with the specified number of bins
hist(x, breaks = bins, col = 'darkgray', border = 'white')
})
output$Generate_PDF_Document <- downloadHandler(
# For PDF output, change this to "report.pdf"
filename = paste0("Highchart Document",format(Sys.Date(),"%d%m%Y"),".html"),
content = function(file) {
# # Copy the report file to a temporary directory before processing it, in
# # case we don't have write permissions to the current working dir (which
# # can happen when deployed).
tempReport <- normalizePath('Test.Rmd')
file.copy(tempReport, "Test.Rmd", overwrite = FALSE)
# Knit the document, passing in the `params` list, and eval it in a
# child of the global environment (this isolates the code in the document
# from the code in this app).
out <- render('Test.Rmd', html_document())
file.rename(out,file)
})
})
ui.r
library(shiny)
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)
),
# Show a plot of the generated distribution
mainPanel(
plotOutput("distPlot"),
downloadButton('Generate_PDF_Document','Generate a PDF Report')
)
)
))
rmarkdown doc:
---
title: "Test"
output:
html_document:
toc: true
toc_depth: 3
toc_float: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example:
```{r pressure, echo=FALSE}
plot(pressure)
```
Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Answer 1

Remove html_document() from render. I have not studied the details, but it looks like it forces override of the yaml front matter.