I have tried to apply the answers given in both this question on saving plots, and this question on downloading reactive outputs without success. I am not sure if my reactive function is outputting the wrong type of data or if my downloadHandler() is not written properly.
Also, the linked questions pass function()s to reactive() which I am warned is deprecated, so I have avoided it here. (The behavior did not change, though.)
ui.R:
library(shiny)
# Define UI for application
shinyUI(pageWithSidebar(
# Application title
headerPanel("App"),
sidebarPanel(
downloadButton("savemap", label="Download Map (Hires)")
),
mainPanel(
tabsetPanel(
tabPanel("Map",
plotOutput("myworld", height="650px",width="750px",
clickId="plotclick")
)
)
)
))
server.R
library(shiny)
library(maps)
library(mapdata)
library(rworldmap)
library(gridExtra)
shinyServer(function(input, output) {
theworld <- reactive({
myplot <- map("world2", wrap=TRUE, plot=TRUE,
resolution=2)
})
output$myworld <- renderPlot({
print(theworld())
})
output$savemap <- downloadHandler(
filename = function() {
paste('fuzzymap-', Sys.Date(), '.png', sep="")
},
content = function(file) {
# function to actually write the image file
# https://stackoverflow.com/questions/14810409/save-plots-made-in-a-shiny-app?rq=1
png(file)
print(theworld())
dev.off()
})
})
The map in the reactive function is plotted sucessfully at startup. The download prompt is generated and a png file downloads, but it contains no data. Additionally, the following non-fatal error is returned, but a search turned up no leads:
Error opening file: 2
Error reading: 9
I think you're confused about what map() returns. You call it for its
side-effect of drawing a plot, not it's return value. Rather than making
it a reactive value, just keep it as an anonymous function.
Here's a simplified version that works for me:
library(shiny)
library(maps)
ui <- bootstrapPage(
plotOutput("myworld", height = 450, width = 750),
downloadButton("savemap", "Download map")
)
theworld <- function() {
map("world2", wrap = TRUE, resolution = 2)
}
server <- function(input, output) {
output$myworld <- renderPlot({
theworld()
})
output$savemap <- downloadHandler(
filename = function() {
paste0("fuzzymap-", Sys.Date(), ".png")
},
content = function(file) {
png(file)
theworld()
dev.off()
}
)
}
runApp(list(server = server, ui = ui))
Related
I have an R shiny app that gets a .csv import from a user and searches the imported data across a built-in data frame, then gives the % match in the output. The UI is very simple, with a few different inputs (import .csv, a slider, and some radio buttons). What I want is to be able to take the reactive table output and print this to a .csv that the user can download to their machine. The server side of the app looks something like this:
server <- function(input, output){
rvals <- reactiveValues()
observeEvent(input$file_1,{
req(input$file_1)
rvals$csv <<- read.csv(input$file_1$datapath, header = TRUE)
#some data processing here
})
output$contents <- renderTable({
if(input$select == 1){
x <- function
}else if(input$select == 2){
x <- function
}else if(input$select == 3){x <- function}
#some more data processing and formatting here
return(x)
},digits = 4)
}
I would like to have the data table x be able to become a .csv that can be downloaded by clicking a download button. In the server, I added the following code, but when I try to download the data it just downloads a blank file and says "SERVER ERROR" in my downloads manager on my machine.
output$downloadData <- downloadHandler(
filename = "thename.csv",
content = function(file){
write.csv(x, file)
}
In the console I also get the error message:
Warning: Error in is.data.frame: object 'x' not found [No stack trace available]
The object you create inside the expression of renderTable is not available outside of it. Instead you could assign it to the reactive values you set up. Below is a working example (note that I have tried to replicate your code so the data will not be available until you click on "Upload CSV", which here just calls mtcars).
library(shiny)
ui = fluidPage(
sidebarPanel(
actionButton(inputId = "uploadCsv", label = "Upload CSV:", icon = icon("upload")),
selectInput(inputId = "preProc", label = "Pre-processing", choices = c("Mean"=1,"Sum"=2)),
downloadButton("downloadData", label = "Download table")
),
mainPanel(
h4("My table:"),
tableOutput("contents")
)
)
server <- function(input, output) {
rvals <- reactiveValues(
csv=NULL,
x=NULL
)
observeEvent(input$uploadCsv,{
rvals$csv <- mtcars # using example data since I don't have your .csv
# rvals$csv <- read.csv(input$file_1$datapath, header = TRUE)
#some data processing here
})
output$contents <- renderTable({
# Assuing the below are functions applied to your data
req(
input$preProc,
!is.null(rvals$csv)
)
if(input$preProc == 1){
rvals$x <- data.frame(t(colMeans(mtcars)))
}else {
rvals$x <- data.frame(t(colSums(mtcars)))
}
return(rvals$x)
},digits = 4)
output$downloadData <- downloadHandler(
filename = "myFile.csv",
content = function(file){
write.csv(rvals$x, file)
}
)
}
shinyApp(ui,server)
EventReactive already outputs a reactive value, you don't need to create an extra reactiveVal, see example below :
library(shiny)
# Define UI
ui <- fluidPage(
# Application title
titlePanel("Test"),
mainPanel(
actionButton("show", "Download"),
textOutput("result")
)
)
server <- function(input, output) {
csvfile <- eventReactive(req(input$show), ignoreNULL = T, {
"Content of file"
})
output$result <- reactive(
paste("result : ",csvfile()))
}
# Run the application
shinyApp(ui = ui, server = server)
I would also avoid to use <<-operator in a reactive expression.
So I want to have a Shiny page which:
A) Allows the user to upload a .xls file;
B) Offers that file back to the user for download as a .csv file;
C) Prints the head of the file in the Shiny app to ensure that it was properly read.
Here is the code I am using:
# Want to read xls files with readxl package
library(readxl)
library(shiny)
## Only run examples in interactive R sessions
if (interactive()) {
ui <- fluidPage(
fileInput("file1", "Choose File", accept = ".xls"),
tags$hr(),
uiOutput("downloader"),
htmlOutput("confirmText", container = tags$h3),
tableOutput("listContents")
)
server <- function(input, output) {
theOutput <- reactiveValues(temp = NULL, df = NULL, msg = NULL, fn = NULL)
observeEvent(input$file1, {
theOutput$fn <- paste('data-', Sys.Date(), '.csv', sep='')
theOutput$temp <- read_xls(input$file1$datapath)
theOutput$msg <- paste("File Contents:")
theOutput$df <- write.csv(theOutput$temp,
file = theOutput$fn,
row.names = FALSE)
})
output$confirmText <- renderText({
theOutput$msg
})
output$listContents <- renderTable({
head(theOutput$temp)
})
output$downloader <- renderUI({
if(!is.null(input$file1)) {
downloadButton("theDownload", label = "Download")
}
})
output$theDownload <- downloadHandler(
filename = theOutput$fn,
content = theOutput$df
)
}
shinyApp(ui, server)
}
The Shiny page renders correctly, it accepts the upload with no problems, it prints out the head of the .csv with no problems, and it creates a properly formatted "data-{today's date}.csv" file in the same directory as the app.R file.
Problem is, when I hit the download button I get the error message:
Warning: Error in download$func: attempt to apply non-function
[No stack trace available]
Can someone tell me what I am doing wrong?
Thanks to the comments above, this is the solution I found (with my comments added, to show where the code changed):
library(readxl)
library(shiny)
if (interactive()) {
ui <- fluidPage(
fileInput("file1", "Choose File", accept = ".xls"),
tags$hr(),
uiOutput("downloader"),
htmlOutput("confirmText", container = tags$h3),
tableOutput("listContents")
)
server <- function(input, output) {
theOutput <- reactiveValues(temp = NULL, msg = NULL)
observeEvent(input$file1, {
# Do not try to automate filename and the write.csv output here!
theOutput$temp <- read_xls(input$file1$datapath)
theOutput$msg <- paste("File Contents:")
})
output$confirmText <- renderText({
theOutput$msg
})
output$listContents <- renderTable({
head(theOutput$temp)
})
output$downloader <- renderUI({
if(!is.null(input$file1)) {
downloadButton("theDownload", label = "Download")
}
})
output$theDownload <- downloadHandler(
# Filename and content need to be defined as functions
# (even if, as with filename here, there are no inputs to those functions)
filename = function() {paste('data-', Sys.Date(), '.csv', sep='')},
content = function(theFile) {write.csv(theOutput$temp, theFile, row.names = FALSE)}
) }
shinyApp(ui, server) }
The fact that content takes an argument (named here "theFile"), which is not called anywhere else, is what was throwing me off.
I am trying to generate a table using the renderTable function in R shiny and then use the downloadHandler function to download that table/data.frame as a csv file. Somehow I keep getting the following error:
An error occured during download:
Error downloading http://127:0:0.1:3001/session/
0303bd426fce88837ae277aa3b406dd/download/downloadData?w= - server
replied: Internal Server Error
Below is an example code where I generate a simple data frame and try to download it using downloadHander:
library(shiny)
# Define UI for data download app ----
ui <- fluidPage(
# App title ----
titlePanel("Downloading Data"),
# Sidebar layout with input and output definitions ----
sidebarLayout(
# Sidebar panel for inputs ----
sidebarPanel(
# Button
downloadButton("downloadData", "Download")
),
# Main panel for displaying outputs ----
mainPanel(
tableOutput("table")
)
)
)
# Define server logic to display and download selected file ----
server <- function(input, output) {
# Table of selected dataset ----
output$table <- renderTable({
data.frame(a =c(1,2,3),b=c("q","s","f"))
})
# Downloadable csv of selected dataset ----
output$downloadData <- downloadHandler(
filename = function() {
paste("test.csv")
},
content = function(file) {
write.csv(output$table, file, row.names = FALSE)
}
)
}
shinyApp(ui,server)
There are a few things that need to be done here:
If your app is going to render data dynamically, then your data should be assigned to some reactive expression.
Now the downloading of the data becomes easy, as you just call the reactive expression written in (1).
Points (1) and (2) above will ensure that the user is downloading the same data that is seen on the screen.
Try the following:
library(shiny)
ui <- fluidPage(
titlePanel("Downloading Data"),
sidebarLayout(
sidebarPanel(downloadButton("downloadData", "Download")),
mainPanel(tableOutput("table"))
)
)
server <- function(input, output) {
data <- shiny::reactive(data.frame(a = c(1, 2, 3), b = c("q", "s", "f")))
output$table <- renderTable(data())
output$downloadData <- downloadHandler(
filename = function() {
paste("test.csv")
},
content = function(file) {
write.csv(data(), file, row.names = FALSE)
}
)
}
shinyApp(ui,server)
You cannot export a renderTable{} as this puts many of the elements into HTML,
you need to previously save the data going into the table and export it
seperately.
dataTable<-data.frame(a =c(1,2,3),b=c("q","s","f"))
output$downloadData <- downloadHandler(
filename = function() {
('test.csv')
},
content = function(con) {
write.table(dataTable,row.names = FALSE,col.names=T, sep=",",con)
},
contentType="csv"
)
Is it possible to set reactiveValues inside the content part of the downloadHandler? I tried it and don't understand the behavior.
A simple example could be a counter showing how often the download button has been clicked:
library(shiny)
ui <- fluidPage(
downloadButton("downloadData", "Download"),
textOutput("nDownloads"),
actionButton("trig", "get number")
)
server <- function(input, output) {
# Our dataset
data <- mtcars
r.nDownloads <- reactiveValues(n=0)
output$nDownloads <- renderText({
input$trig
paste("number of downloads:", r.nDownloads$n)
})
output$downloadData <- downloadHandler(
filename = function() {
paste("data-", Sys.Date(), ".csv", sep="")
},
content = function(file) {
r.nDownloads$n <- r.nDownloads$n + 1
write.csv(data, file)
}
)
}
shinyApp(ui, server)
If the download button is clicked, the textOutput is grayed out, but not updated. I added an action button as a trigger to force the renderText to be updated. Surprisingly (at least to me) that works: the correct number is shown.
So, somehow the reactiveValue is changed by the downloadHandler, but its dependencies are only invalidated, not updated.
Of course, the proper way to do it would be making the "data"-object reactive and doing the counting there. But I'm curious how the described behavior can be explained.
EDIT:
OK, now I get really confused: I tried what I mentioned above: making "data" reactive and doing the counting there. This could not be simple counting of downloads anymore, because the data-reactive gets only recalculated if it's invalid.
Here is an example with an additional input for the invalidation of "data":
library(shiny)
ui <- fluidPage(
numericInput("nRows", label = "nRows", min=1, max=32, value=15),
downloadButton("downloadData", "Download"),
textOutput("nDownloads")
)
server <- function(input, output) {
r.nDownloads <- reactiveValues(n=0)
# Our dataset
data <- reactive({
isolate({
r.nDownloads$n <- r.nDownloads$n + 1
})
mtcars[1:input$nRows,]
})
output$nDownloads <- renderText({
paste("number of downloads:", r.nDownloads$n)
})
output$downloadData <- downloadHandler(
filename = function() {
paste("data-", Sys.Date(), ".csv", sep="")
},
content = function(file) {
write.csv(data(), file)
}
)
}
shinyApp(ui, server)
But still, I see a similar behavior: Clicking the download button grays the text out, changing "nRows" makes the expected number of downloads (which is now downloads after a change in nRows ;-)) to show up.
Now it gets an actual problem for me: In my real app, a rather complex Excel file can be downloaded. While preparing and formatting the Excel file there can occur events that should lead to some reaction of the app. That's why the download should trigger something. The alternative I can see is, to prepare the Excel file before the user clicks on download (what I would like to avoid, because this can take a few seconds depending on the complexity of the file/formatting).
Am I missing something obvious? If not, I'd appreciate any ideas, how the download event can trigger something in the rest of the app.
The solution is to remove the isolation of the reactiveValues as this prevents the counter from being updated until the numericInput is triggered. This is because data() is dependent on input$nrows.
library(shiny)
ui <- fluidPage(
numericInput("nRows", label = "nRows", min = 1, max = 32, value = 15),
downloadButton("downloadData", "Download"),
textOutput("nDownloads")
)
server <- function(input, output) {
r.nDownloads <- reactiveValues(n = 0)
# Our dataset
data <- reactive({
r.nDownloads$n <- r.nDownloads$n + 1
mtcars[1:input$nRows,]
})
output$nDownloads <- renderText({
paste("number of downloads:", r.nDownloads$n)
})
output$downloadData <- downloadHandler(
filename = function() {
paste("data-", Sys.Date(), ".csv", sep = "")
},
content = function(file) {
write.csv(data(), file)
}
)
}
shinyApp(ui, server)
With regards to the deeper problem, it would be inefficient to constantly prepare a complex Excel file if there is no guarantee that the user would download the file. What you can try to do is:
Keep your data in a reactive method (e.g. data()).
Write a method to prep your data for downloading (e.g. prepExcel(data)) which returns your prepped data.
Pass (1) and (2) into the content of the downloadHandler() like this: write_xx(prepExcel(data())) or pipe the data into the write_xx function like this data() %>% prepExcel() %>% write_xx() where xx is the method used to output your final file e.g. write_xlsx or write_csv etc.
I hope this helps.
I'm currently working on image processing application using R Shiny It uploads an image using file upload and then I need to read the image to do the image processing operations. server.R file is as follows.
library(shiny)
library(EBImage)
library(imager)
library(jpeg)
function(input, output) {
observe({
file_path <- input$files
if (is.null(file_path))
return(NULL)
file_path$datapath <- gsub("\\\\", "/", file_path$datapath)
img <- readImage(file_path$datapath)
equalized <- equalize(img,range = c(0, 1), levels = 256)
output$text <- renderText({
file_path$datapath
})
output$img <- renderImage({
list(src = file_path$datapath,
contentType = "image/jpg",
width = "50%",
height = "auto",
alt = "This is alternate text")
})
})
}
But this gives me the following error.
Warning: Error in readImage: Please supply at least one filename.
Stack trace (innermost first):
57: readImage
56: observerFunc
I managed to plot an equalized image using raster method. Here are some tips/tricks:
You put everything inside an observer which is a pretty bad idea, so I got rid of that.
Use req() when checking whether a file is uploaded, UI is rendered, etc instead of an if statement. `
if (is.null(file_path)) return(NULL)
There is no need to assign input$files to a variable, you can call input$files$datapath. Also gsub() is not needed in this case.
file_path <- input$files
file_path$datapath <- gsub("\\\\", "/", file_path$datapath)
equalized is calculated, but you don't use it anywhere.
Solution
Checking with req() whether a file is uploaded.
Get the extension of the file (splitting by ., getting the last element)
Plot the equalized image using the display() function with method = "raster".
Print datapath which points to a temp dir/file
See:
library(shiny)
library(EBImage)
library(imager)
library(jpeg)
ui <- fluidPage(
fileInput("files", "Upload a file"),
plotOutput("img"),
textOutput("txt")
)
server <- function(input, output) {
output$img <- renderPlot({
req(input$files)
st <- strsplit(input$files$name, split = "[.]")[[1]]
extension <- st[length(st)]
display(equalize(readImage(input$files$datapath, type = extension), range = c(0, 1), levels = 256), method = "raster")
})
output$txt <- renderText({
input$files$datapath
})
}
shinyApp(ui, server)
Using EBImage we can load an image into Rshiny and use it for further processing. Below code allows the user to upload an image and then same is displayed on shiny screen back.
library(shiny)
library(EBImage)
upload_image <- list()
ui <- fluidPage(
fileInput("file1", "Upload an Image"),
plotOutput("img")
)
server <- function(input, output) {
output$img <- renderPlot({
req(input$file1)
upload_image[[1]] <- readImage(input$file1$datapath)
plot(upload_image[[1]])
})
}
shinyApp(ui , server)