Shiny R - download the result of a table - r

I am new to Shiny and I have created a really simple shiny app:
library(shiny)
ui <- fluidPage(
fluidRow(column(7,dataTableOutput('dto')))
)
server <- function(input,output){
output$dto <- renderDataTable({MYTABLE})
}
runApp(list(ui=ui,server=server))
Is there any way to put an option to download the result of the table (doesn't matter if is CSV, XLSX...)
cheers

That's pretty easy with downloadButton() or downloadLink() in combination with downloadHandler if you make the data itself a reactive expression. Then you can download whatever you send to output using the same reactive expression.
A small example:
library(shiny)
ui <- fluidPage(
# This one is linked by the id 'download'
downloadButton('download',"Download the data"),
fluidRow(column(7,dataTableOutput('dto')))
)
server <- function(input,output){
# Reactive expression with the data, in this case iris
thedata <- reactive(iris)
output$dto <- renderDataTable({thedata()})
output$download <- downloadHandler(
filename = function(){"thename.csv"},
content = function(fname){
write.csv(thedata(), fname)
}
)
}
runApp(list(ui=ui,server=server))
Keep in mind:
the argument content of downloadHandler must be a function producing a file! It should take one argument for the connection/file name. In this example it is a csv file, but for eg images you can use png() and dev.off(), for ggplots you can use ggsave(), ...
the argument filename does not have to be a function, but I found it works
better that way. Especially when working with reactive expressions for the file name.
you link the downloadHandler and the downloadButton through the output list: the id of downloadButton is the name of the output element returned by downloadHandler.
EDIT:
Some people try to use download.file() for this, but that's wrong as well. The function download.file() works when used on the user side, not the server side. It lets you download files from the internet to the computer that is calling the function. If you'd use that in a Shiny application, it would work when run locally. That's because user and server are the same machine. However, when deploying your app on a Shiny Server, download.file() would essentially be downloading files TO the server, not from.

A slightly alternative solution based directly on the datatable / DT extension buttons.
I am shamelessly borrowing the example data from Joris...
library(shiny)
library(DT)
ui <- fluidPage(
# This one is linked by the id 'download'
fluidRow(column(7,dataTableOutput('dto')))
)
server <- function(input,output){
# Reactive expression with the data, in this case iris
thedata <- reactive(iris)
#the extensions parameter coupled with the options list does the trick
output$dto <- renderDataTable(thedata(), extensions = 'Buttons',
options = list(dom = 'Bfrtip',
buttons = c('copy', 'csv', 'excel', 'pdf', 'print'))
)
}
runApp(list(ui=ui,server=server), launch.browser=TRUE) #now runs by default in the external browser.
This will work with different outputs and personally I like the cleaner look. Just make sure that you are running the demo in the external browser. Otherwise it won't work.

I have to execute the app in the browser because the filename isn't working. I use
runApp(list(ui=ui,server=server),launch.browser = T)
and it works perfectly for me.
If you don't want to use launch.browser=TRUE you can write the filename and the extension for example .csv at the end of the filename when you use the download button in the shiny app.

Related

How can I import certain file types in R

Sorry for what seems like a basic question, I'm very new to R and programming in general. I want to be able to determine what file type was picked from a file. For example, in this code I need to have two separate buttons for importing a CSV or excel file:
observeEvent(input$CSV, {
Table <- read.table(file.choose(), header=TRUE, sep=",")
output$ImportedTable <- DT::renderDataTable(Table)
})
observeEvent(input$Excel, {
Table <- read_excel(file.choose())
output$ImportedTable <- DT::renderDataTable(Table)
})
(input$Excel/CSV is the output of an actionButton in the main pannel)
Ideally, I'd like to only require one button instead of two, and have the program able to determine what file type was chosen, and import it accordingly. and ideally, I'd like to be able to sort what data types are available to choose from when importing, since currently it allows the user to pick all file types, instead of just ones in a table format. I'd appreciate any help, thanks!
You seem to work with shiny (this is an important bit of information missing from your main post).
In shiny you can use fileInput to restrict the format of input files. Here is a minimal reproducible example.
library(shiny)
ui <- fluidPage(
fileInput(inputId = "file_csv", label = "CSV file", accept = ".csv"),
fileInput(inputId = "file_xlsx", label = "XLSX file", accept = ".xlsx"),
)
server <- function(input, output) {
}
shinyApp(ui = ui, server = server)
Note that you can see the effect of accept when opening the app in your browser of choice. RStudio's native app window or Viewer Pane does not seem to respect the accept argument.

List of file paths to iteratively pass through sourced python function in Shiny

I have come up with a python function that I have confirmed works just fine. I am trying to put this into a Shiny app using Shiny's reticulate. I am not super familiar with Shiny but need to use it anyhow.
To give a bit of background on what I am doing, I've written some python code that takes takes multiple files and matches strings based on one common list of strings. This code works fine when I run the python files on my machine.
I need to make this available to others using a shiny app, where they can upload their files, then have the app run the underlying python code.
So far, I have set up the shiny app so that it can take in multiple files. I am having a hard time thinking about how I can use reactive to make a list of the file path names to then send to my python code (which includes a step to open and read the file) so it can do its thing.
This is the code that I have for my app thus far:
library(shiny)
library(shinyFiles)
# define UI
ui <- fluidPage(
titlePanel('Counter of Gendered Language'),
fileInput("upload", "Choose a folder",
multiple = TRUE,
accept = c('text')),
tableOutput('text'),
downloadButton('output', 'Download Count File .csv'))
# define server behavior
server <- function(input, output){
# Setup
#* Load libraries
library(reticulate)
#* Use virtual environment for python dependencies
use_virtualenv('file/path/py_venv', required = TRUE)
#* Source code
source_python('code/counting_gendered_words.py')
#* Load list of words to match raw text against
dictionary <- read.csv('data/word_rating.csv')
text <- reactive(
list <- list.files(path = input$upload[['name']])
)
output$counted <- gendered_word_counter(dictionary, text())
output$downloadData <- downloadHandler(
filename = function(){
paste0(input$upload, ".csv")
},
content = function(file){
vroom::vroom_write(text$counted, file)
}
)
}
# Run the application
shinyApp(ui = ui, server = server)
What it tells me when I run this app is that:
Error : Operation not allowed without an active reactive context.
You tried to do something that can only be done from inside a reactive consumer.
So what I am wanting to do is basically just pass each file name that someone uploads to the app and pass that file's name into my gendered_word_counter() python function.
How would I go about this?
I'm super confident that I just am being a newbie and it is probably a super simple fix. Any help from those who are more comfortable with Shiny would be much appreciated!
Edit: I notice that my code is only calling the names of the files which is meaningless for me without the contents of the uploaded files! Would it be better if I read the files in the shiny app instead of in my .py file?
I can't reproduce the app without the python code, but i can see that this line:
output$counted <- gendered_word_counter(dictionary, text())
has a reactive object (text()) being called with no reactive context. It should be wrapped in observe or observeEvent.
observe({
output$counted <- gendered_word_counter(dictionary, text())
})
Also let's add the parenthesis here:
content = function(file){
vroom::vroom_write(text()$counted, file)
}

display.mode = 'showcase' in shinyApp() call - no code shown

I would like to be able to use display.mode = 'showcase' in an app run with the shinyApp() function call. According to the docs I should be able to pass any arguments that go runApp() through the options argument. The showcase mode works (the window is split) but it does not show the code. What's interesting is that if I run runExample("01_hello") everything works fine. I'm using shiny 1.0.5.
Code:
library(shiny)
ui <- fluidPage(
titlePanel("Sample App"),
sidebarLayout(
sidebarPanel(
selectInput("data", label = "Data set",
choices = c("mtcars", "iris"))
),
mainPanel(
tableOutput("table")
)
)
)
server <- function(input, output) {
data <- reactive({
get(input$data, 'package:datasets')
})
output$table <- renderTable({
head(data())
})
}
shinyApp(ui, server, options = list(display.mode = 'showcase'))
Output:
I was having the same issue. I had the app.R file and created the DESCRIPTION file using notepad but couldn't deploy a shinyApp with the code. Then I copied the DESCRIPTION file from shiny\examples\01_hello and noticed this:
Turns out my file had a TXT extension, so Shiny wasn't reading it as a metadata file. Once I used the correct DESCRIPTION file (which you can edit using notepad), everything worked out fine.
This is more of an addendum to Gus_est's answer, since I had the same problem and wasn't able to get it run right from there.
Create a file inside the directory your app.R-file resides in, e.g. a txt-file. Write into the file what display mode is to be used using Debian Control file format. In our case it would look like that (Title is not necessary):
Title: My App
DisplayMode: Showcase
Then rename the file DESCRIPTION without providing a file ending. Ignore the warning.
When you run the app now, it will always be in display mode "showcase", you can override this only inside the runApp()-statement. So I find the documentation to be misleading.
Check your current working directory. This problem seems to occur, if the working directory is not set to the folder with the app code.

Uploading picture to the knitr document via Shiny

I am using combination of Shiny and knitr to create PDF documents.
Currently I want to add feature that will allow user to upload picture that will be placed within the created document. However, I am really stuck because I am unable to get the path of the input picture. Could anyone help me with that?
Simple example:
Application:
library(knitr)
library(shiny)
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
fileInput("picture", label = 'Picture'),
downloadButton('report', label = 'Download PDF')
),
mainPanel()
)
)
server <- function(input,output){
picture <- reactive({
input$picture[,4]
})
output$report = downloadHandler(
filename = "test.pdf",
content = function(file){
picture = picture()
out = knit2pdf(input = 'test.Rnw', compiler = 'xelatex', clean = TRUE)
file.rename(out, file)
},
contentType = 'application/pdf'
)
}
shinyApp(ui = ui, server = server)
and the .Rnw document:
\documentclass{article}
\begin{document}
Put picture here:
<<echo = FALSE , message = F, results='asis'>>=
cat(paste('\\includegraphics[height=3in]{', picture,'}'))
#
\end{document}
Part '\includegraphics[height=3in]{', picture,'} is obviously causing the problem, because I do not know the picture path only temporary one.
You said you were working with Shiny Server, then you should be okay with the full path of the picture, even if it is in a temporary directory (because currently Shiny Server only works on Linux, and LaTeX should be okay with Linux file paths like /tmp/...../yourfile.png). The problem is perhaps the datapath (i.e. input$picture[, 4]) does not have the file extension, so LaTeX could not recognize it. You may try to retrieve the filename extension of the original file, and copy the uploaded picture to a temp file with the same extension, e.g.
picture <- reactive({
path1 <- input$picture$datapath
path2 <- tempfile(fileext = gsub('^(.*)([.].+)$', '\\2', input$picture$name))
file.copy(path1, path2, overwrite = TRUE)
path2
})
i see a solution in two ways:
1) copy the temporary file to a folder of your choice and use that image:
observe({
if (is.null(input$picture)) return()
picture<-"your/final/path/to/disk/uploadImage.jpg" # OR do a PASTE with the PATH and the upload file name
file.copy(input$picture$datapath, picture)
if(file.exists(picture)){
# PROCESS THE IMAGE IF NEEDED
}
picture<<-picture # sometimes needed to R to see the variable outside the observe scope
})
2) if you (in this case the R session) are not allowed to write to disk you can turn the image into a base64 variable and include that into your Knitr document (or save it to a database as a string). This takes the Knitr/HTML route if you are willing to take that detour. (R studio running from a server almost always has a lot of restrictions in reading/writing that you can only handle as an ADMIN. And the server runs the shiny session as RStudio and not you so Rstudio must have the read/write permissions needed if you run the Shiny app as an automatic Rstudio Shiny session and not run it directly form RStudio using RUN)
Make sure the base64 is readable by R ouside the 'observe' or 'if' scope again by using '<<-' together with '<-'. Scoping is quite something special with R so be sure to test it properly.
You should dive into this (base64) with sites like:
https://github.com/yihui/knitr/issues/944
https://github.com/yihui/knitr/blob/master/R/utils-base64.R

Adding an Email button in Shiny, using TableTools or otherwise

The code below produces a DataTable output that I'd like to have it emailed using an Email button, similar to the Export button created below. Is there an easy way to add a button so that when you click, it pops up Microsoft Outlook to send the datatable as an attachment, say in csv format?
Also, please click here and here to help with a similar questions.
#Load required packages
require(shiny)
#Create a dataframe
df <- data.frame(random=1:160)
server <- function(input,output,session){
#Display df using DataTable and apply desired options
output$display <- renderDataTable({df},
option=list(pageLength=100,
"dom" = 'T<"clear">lfrtip',
"tableTools" = list(
"sSwfPath" = "//cdn.datatables.net/tabletools/2.2.3/swf/copy_csv_xls_pdf.swf",
"aButtons" = list(list("sExtends" = "csv","oSelectorOpts"=list("page"="all"),"sButtonText" = "Export","aButtons" ="csv")))
)
)
}
ui <- shinyUI(fluidPage(
#Add a title
h1('Testing TableTools'),
#Add required JS libraries
tagList(
singleton(tags$head(tags$script(src='//cdn.datatables.net/1.10.4/js/jquery.dataTables.min.js',type='text/javascript'))),
singleton(tags$head(tags$script(src='//cdn.datatables.net/tabletools/2.2.3/js/dataTables.tableTools.min.js',type='text/javascript'))),
singleton(tags$head(tags$link(href='//cdn.datatables.net/tabletools/2.2.3/css/dataTables.tableTools.css',rel='stylesheet',type='text/css')))
),
mainPanel(
#Display results
dataTableOutput('display')
)
))
shinyApp(ui = ui, server = server)
A quick way is to use mailto(which works well with Outlook).
The mailto would need to be inside an HTML() tag for shiny to render it.
HTML(
<a href="mailto:hello#rshiny.com?
body='Hello,World! Check out my data.'
&subject='Data'
&attachment='\\myfolder\shinyData.csv'">click here for email!</a>
)
There are two hypothetical ways to do this.
Have the mailto in ui.R
The code would need to download the datatable at the user's end (probably in the temp folder), and attach it there.
Have the mailto in server.R
You'll need the csv file already saved on your server in order to load it as an attachment. You would need to use the above code inside a renderUI() and also pass the file from your server to the user's end.
There is a downloadHandler() function which allows users to download from the server which could be of use for the above.
I've never tried passing attachments around as you are trying, however the above logic should both allow you to create an email, and get you on the right path to attaching files.

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