Generating downloadable reports from Shiny app - r

Question

I made an R script that allows to get an R Markdown report with a certain type of dataset. Now I would like other people to be able to use this script in order to get an automated report with their data but without using this script (especially for people who don't master R).
I try to go through Shiny hoping to make an interface that loads a dataset and would make my script automatically but I can't make the link between Shiny and my Rmd.
How can I tell my Rmd that the dataset to be processed is not the one that my Rmd script was going to look for in a directory but the one that was loaded on the Shiny interface?
Thanks
Here is the Shiny script with my Rmd called "traitemant_bis.Rmd" :
library(shiny)
library(rmarkdown)
ui <- fluidPage(
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput(
inputId = "file1", label = "Choose CSV File",
multiple = FALSE,
accept = c("text/csv", "text/comma-separated-values,text/plain", ".csv")
),
radioButtons("format", "Document format", c("PDF", "HTML", "Word"), inline = TRUE)
),
mainPanel(
tableOutput("contents"),
downloadButton("downloadReport")
)
)
)
server <- function(input, output) {
dataset <- reactive({
req(input$file1)
read.csv(file = input$file1$datapath,
na.strings = ".",
sep = ";",
header = TRUE,
nrows=10)
})
output$contents <- renderTable({
req(dataset())
head(dataset())
})
output$downloadReport <- downloadHandler(
filename = function() {
paste("my-report", sep = ".", switch(
input$format, PDF = "pdf", HTML = "html", Word = "docx"
))
},
content = function(file) {
src <- normalizePath("traitemant_bis.Rmd")
owd <- setwd(tempdir())
on.exit(setwd(owd))
file.copy(src, "traitemant_bis.Rmd", overwrite = TRUE)
out <- render("traitemant_bis.Rmd", switch(
input$format,
PDF = pdf_document(), HTML = html_document(), Word = word_document()
))
file.rename(out, file)
}
)
}
shinyApp(ui, server) ```

Answer 1

I'm giving a simple example showing how you can achieve this. Basically, you can pass any of your data from shiny to Rmd as params.
If you have multiple data frames or any data convert them to a single list and pass as params, you can extract individual data later in the RMarkdown
app.R
library(shiny)
ui <- fluidPage(
# Application title
titlePanel("RMD example"),
downloadButton("btn", "Generate Report")
)
# Define server logic required to draw a histogram
server <- function(input, output) {
data <- reactive({
mtcars
})
output$btn <- downloadHandler(
filename = function(){"myreport.docx"},
content = function(file) {
tempReport <- file.path(tempdir(),"markdown.Rmd")
file.copy("markdown.Rmd", tempReport, overwrite = TRUE)
rmarkdown::render("markdown.Rmd", output_format = "word_document", output_file = file,
params = list(table = data()), # here I'm passing data in params
envir = new.env(parent = globalenv()),clean=F,encoding="utf-8"
)
}
)
}
# Run the application
shinyApp(ui = ui, server = server)
Rmd file
---
title: "Untitled"
author: "Mohan"
date: "2/17/2021"
params:
table: [some object]
output: word_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$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}
params$table -> data
data
summary(data)
```