Table of contents in render markdown by shinyapp - r

Question

I have problems generating table of contents in the markdown generated by my shinyapp.
I have tried to set in the YAML toc = TRUE but it doesn't work.
the app is something like this, an interface where some data is uploaded and a markdown where some graphics are rendered.
the problem is that when generating the pdf, html or word the table of contents is not generated.
app.R
library(shiny)
library(dplyr)
library(qcc)
library(ggplot2)
library(readxl)
library(kableExtra)
library(knitr)
shinyApp(ui =
fluidPage(fileInput("file", "Cargar Datos", multiple = FALSE),
radioButtons('format', 'Formato del documento', c('PDF', 'HTML', 'Word'),inline = TRUE),
downloadButton('downloadReport')),
server = function(input, output, session){
myData <- reactive({ infile <- input$file
if(is.null(infile)) return(NULL)
data <- read_excel(infile$datapath)
data})
plotData <- function(){plot(myData}
output$downloadReport <- downloadHandler(
filename = function() {
paste('my-report', sep = '.', switch(
input$format, PDF = 'pdf', HTML = 'html', Word = 'docx'
))
},
content = function(file) {
src <- normalizePath('report.Rmd')
# temporarily switch to the temp dir, in case you do not have write
# permission to the current working directory
owd <- setwd(tempdir())
on.exit(setwd(owd))
file.copy(src, 'report.Rmd', overwrite = TRUE)
library(rmarkdown)
out <- render('report.Rmd', switch(
input$format,
PDF = pdf_document(), HTML = html_document(), Word = word_document()
))
file.rename(out, file)
}
)
########################################
####
})
report.Rmd
---
title: "title"
subtitle: "subtitle"
output:
toc: true
toc_depth: 4
number_sections: true
author:
- "a1"
- "a2"
date: "`r format(Sys.Date(), '%B %d, %Y')`"
params:
p1: "p1"
p2: "p2"
---
# section1
## section1.1
# section2
```{r}
plotData()

Answer 1

Try passing the options as arguments to the rendering function, e.g.
rmarkdown::render('report.Rmd', rmarkdown::pdf_document(toc = TRUE, toc_depth = 4, number_sections = TRUE))
answered by stefan in a comment on the question.