I have a shiny app where you can upload some raw data and build a summarizedExperiment (let's call it RAW) or you can upload an already processed summarizedExperiment (let's call it FINAL). Now I need to save in a reactive object RAW or FINAL. I tried something like this:
sumexp_all = reactive({
if(!is.null(RAW())){
list(sumexp_data = RAW()$sumexp_data, sumexp_data_mean = RAW()$sumexp_data_mean, replicates = RAW()$replicates)
}else if(!is.null(input$finalsumexpinput)){
readRDS(file = input$finalsumexpinput$datapath)
}else{
NULL
}
})
But in this case it works only if I have RAW (if I don't have RAW (so should be NULL since there are many req() in the pipeline) and I want to upload FINAL, nothing happens). If reverse the if conditions (before FINAL and then RAW) I can upload the FINAL. What's wrong? Is it correct to evaluate a reactive with is.null()?
I tried something else like this:
sumexp_all = reactive({
checkerror <- tryCatch(RAW(), error = function(e) "empty")
if(checkerror != "empty"){
list(sumexp_data = RAW()$sumexp_data, sumexp_data_mean = RAW()$sumexp_data_mean, replicates = RAW()$replicates)
}else if(!is.null(input$finalsumexpinput)){
readRDS(file = input$finalsumexpinput$datapath)
}else{
NULL
}
})
But the shiny app crashes and returns this error:
Warning: Error in if: argument is of length zero
And that's weird because if I print checkerror it correctly returns "empty" if's empty.
UPDATE:
I made some testing in order to find where is the problem, and the problem is with the RAW() reactive. Basically I tried this code to find the problem:
checkraw = reactive({
if(is.null(RAW())){
"raw is null"
}else{
"raw is not null"
}
})
checkinp = reactive({
if(is.null(input$finalsumexpinput$datapath)){
"input non loaded"
}else{
"input loaded"
}
})
output$printcheck= renderPrint({
paste(checkraw(), ",", checkinp())
})
So what I expect from this code is that if RAW() doesn't exist and I uplaod the rds file, it' printed "raw is null, input loaded", but what happens is that nothing is displayed.
If RAW() exists then it's correctly printed "raw is not null, input not loaded"
Then I tried to print only checkinp() (removing the checkraw() reactive) and then checkinp() is correctly printed.
So it seems to me that the problem is in the evaluation of the RAW() reactive. Do you think that the problem could be that RAW() depends on others reactive variables (so there is a req() inside it).
EDIT:
Here is a reproducible example.
ui <- shinyUI(pageWithSidebar(
headerPanel("check"),
sidebarPanel(
actionButton("Button", "enable raw"),
textInput("text", "write something", "something..."),
br(),
),
mainPanel(
verbatimTextOutput("printcheck"),
verbatimTextOutput("checkfin")
)
))
server <- shinyServer(function(input, output) {
stepa = eventReactive(input$Button, {
rnorm(100)
})
stepb = reactive({
req(stepa())
stepa() * 100
})
output$printcheck = renderPrint({
is.null(stepb())
})
fin = reactive({
if(!is.null(stepb())){
stepb()
}else{input$text}
})
output$checkfin = renderPrint({
fin()
})
})
shinyApp(ui=ui,server=server)
As you can see output$checkfin is printed ONLY if stepb() is not null even if in this case should be printed input$text
I posted the problem on the shiny github page. For those interested, here's the answer.
https://github.com/rstudio/shiny/issues/3533
Related
I have a shiny app which has many text inputs. I could not get the save data part right, for example, to save to a local drive. Any suggestions?
server = function(input, output) {
values <- reactiveValues()
#Initial Dataframe
values$df <- data.frame(matrix(ncol=4,nrow=0, dimnames=list(NULL, c("Name", "date","Traning", "certificate"))))
FinalData =observe({
if(input$submit >0) {
isolate(values$df <- rbind(values$df,data.frame("name" = input$name,"date" = input$date,
"training" = input$training, "certificate" = input$certificate)))
# saveRDS(values$df)
# saveRDS(FinalData)
}})
#display the inputs
output$Combined_table = renderDataTable({values$df})
}
)
Try this demonstration:
library(shiny)
.log <- function(...) message(format(Sys.time(), format = "[ %H:%M:%S ]"), " ", ...)
.read <- function(path) if (file.exists(path)) return(readRDS(path))
shinyApp(
ui = fluidPage(
textInput("txt", "Text: "),
actionButton("btn", "Submit"),
tableOutput("tbl")
),
server = function(input, output, session) {
.log("hello world")
rv <- reactiveValues()
rv$df <- data.frame(row = 0L, word = "a", stringsAsFactors = FALSE)[0,]
observeEvent(req(input$btn), {
.log("submit!")
rv$df <- rbind(rv$df,
data.frame(row = input$btn, word = input$txt,
stringsAsFactors = FALSE))
.log("saveRDS: ", nrow(rv$df))
saveRDS(rv$df, "local.rds")
})
filedata <- reactiveFileReader(1000, session, "local.rds", .read)
output$tbl <- renderTable(filedata())
}
)
The engineering of this app:
I use a reactiveValues like you did, in order to keep the in-memory data. (Note: iteratively adding rows to a frame is bad in the long-run. If this is low-volume adding, then you're probably fine, but it scales badly. Each time a row is added, it copies the entire frame, doubling memory consumption.)
I pre-fill the $df with a zero-row frame, just for formatting. Nothing fancy here.
observe and observeEvent do not return something you are interested in, it should be operating completely by side-effect. It does return something, but it is really only meaningful to shiny internals.
saveRDS as you do, nothing fancy, but it works.
I added a shiny::reactiveFileReader in order to demonstrate that the file was being saved. When the shiny table shows an update, it's because (1) the data was added to the underlying frame; (2) the frame was saved to the "local.rds" file; then (3) reactiveFileReader noticed that the underlying file exists and has changed, causing (4) it to call my .read function to read the contents and return it as reactive data into filedata. This block is completely unnecessary in general, just for demonstration here.
I create a function .read for this reactiveFileReader that is resilient to the file not existing first. If the file does not exist, it invisibly returns NULL. There may be better ways to do this.
I am working on building a shiny App. I have used some filters and rendered a data frame and the data frame changes dynamically as per the user input. But I cannot store a particular column value from a data frame into a vector. I need to store the reactive output every time into a vector so that I can use the values later again. Here the values are stored in text_vec and i need to pass that into the API but I cannot access the values from text_vec and i have to pass the updated values every time into the API
library(dplyr)
library(shiny)
shinyApp(ui = fluidPage(
sidebarLayout(
sidebarPanel(
selectInput(inputId = "cyl",
label = "Number cylinders:",
choices = c("all",sort(unique(mtcars$cyl))),
selected = "all"),
actionButton("capture",
"capture value")
), # closes sidebarPanel
mainPanel(
tableOutput("text"),
tableOutput("text2"),
tableOutput("text3"),
tableOutput("table")
) # closes mainPanel
) # closes sidebarLayout
), # closes fluidPage
server = function(input, output) {
# some example reactive data
cars_react <- reactive({
mtcars %>%
filter(cyl == input$cyl | input$cyl == "all")
})
# simply global assignment of a reactive vector
observeEvent(cars_react(), {
# here is a globally assigned vector taken from the reactive data
# reused in a render statement it will not react to change, since it is not reactive
test_vec3 <<- unique(cars_react()$hp)
})
# here a file is written to the working directory of your shiny app
# everytime cars_react() changes write (and overwrite) vector to a file
observeEvent(cars_react(), {
test_vec = unique(cars_react()$hp)
saveRDS(test_vec, file = "test_vec.Rdata")
})
# same as above but the file is gradually growing and not overwritten
# everytime cars_react() changes add vector to a (over several sessions growing) list
observeEvent(cars_react(), {
test_vec2 = unique(cars_react()$hp)
if (file.exists("test_list.Rdata")) {
temp = readRDS("test_list.Rdata")
test_list = c(temp, list(test_vec2))
} else {
test_list = list(test_vec2)
}
saveRDS(test_list, file = "test_list.Rdata")
})
# here we access the reactive data with isolate and make it non-reactive, but can update the values through a button click
text_vec <<- eventReactive(input$capture, {
isolate(unique(cars_react()$hp))
})
# output of our reactive data as table
output$table <- renderTable({
cars_react()
})
# text output of globally assigned non-reactive vector test_vec3 (not changing!)
output$text <- renderText({
test_vec3
})
# you can capture values of reactives with isolate, but then, they don't change anymore
# text output of isolated formely reactive vector unique(cars_react()$hp (not changing!)
output$text2 <- renderText({
isolate(unique(cars_react()$hp))
})
# text output of new reactive vector (changes when input$capture button is clicked)
output$text3 <- renderText({
text_vec()
})
for (i in text_vec)
{
url = "https://oscar.com/prweb/PRRestService/"
parameters<-'{
{
"Reference":"Account"
,"ReferenceValue":""
}'
b<-fromJSON(parameters)
b["ReferenceValue"]=i
r <- POST(url, body = parameters,encode = "json")
r_c<-toJSON(content(r))
print(r_c)
}
}
)
A simple way to get a data frame to persist across all environments used within your Shiny app, is to use the '<<-' assignment instead of the '<-" assignment. This is not a great programming technique, but it may be what you're hoping to find.
# To get a data frame to persist, use
a <<- b
# instead of
a <- b
** Updated answer **
Based on your updated answer, I would wrap you API call into an observeEvent which gets triggered once the action button is pressed. Since you do not provide a working example with some real code, I am not sure whether the example below is of help. I further assume that your for loop is correct and working (on my end, I cannot know without a real API and some real values).
library(dplyr)
library(shiny)
library(httr)
library(jsonlite)
shinyApp(ui = fluidPage(
selectInput(inputId = "cyl",
label = "Number cylinders:",
choices = c("all",sort(unique(mtcars$cyl))),
selected = "all"),
actionButton("capture",
"capture value")
), # closes fluidPage
server = function(input, output) {
# some example reactive data
cars_react <- reactive({
mtcars %>%
filter(cyl == input$cyl | input$cyl == "all")
})
# here we access the reactive data with isolate and make it non-reactive, but can update the values through a button click
observeEvent(input$capture, {
for (i in unique(cars_react()$hp))
{
url = "https://oscar.com/prweb/PRRestService/"
parameters<-'{
"Reference":"Account"
,"ReferenceValue":""
}'
b<-fromJSON(parameters)
b["ReferenceValue"]=i
r <- POST(url, body = parameters,encode = "json")
r_c<-toJSON(content(r))
print(r_c)
}
})
}
)
Old answer
It is not clear from your question how, where and how often you want to use the vector of your reactive data frame. But it is an important question, since the concept of reactivity and how to access it is very hard to grasp when you come from a pure non reactive R environment.
Below is a simple example app which shows how to access vectors in reactive data frames, and how they could be used.
I hope it helps to get a better understanding of reactivity in shiny.
library(dplyr)
library(shiny)
shinyApp(ui = fluidPage(
sidebarLayout(
sidebarPanel(
selectInput(inputId = "cyl",
label = "Number cylinders:",
choices = c("all",sort(unique(mtcars$cyl))),
selected = "all"),
actionButton("capture",
"capture value")
), # closes sidebarPanel
mainPanel(
tableOutput("text"),
tableOutput("text2"),
tableOutput("text3"),
tableOutput("table")
) # closes mainPanel
) # closes sidebarLayout
), # closes fluidPage
server = function(input, output) {
# some example reactive data
cars_react <- reactive({
mtcars %>%
filter(cyl == input$cyl | input$cyl == "all")
})
# simply global assignment of a reactive vector
observeEvent(cars_react(), {
# here is a globally assigned vector taken from the reactive data
# reused in a render statement it will not react to change, since it is not reactive
test_vec3 <<- unique(cars_react()$hp)
})
# here a file is written to the working directory of your shiny app
# everytime cars_react() changes write (and overwrite) vector to a file
observeEvent(cars_react(), {
test_vec = unique(cars_react()$hp)
saveRDS(test_vec, file = "test_vec.Rdata")
})
# same as above but the file is gradually growing and not overwritten
# everytime cars_react() changes add vector to a (over several sessions growing) list
observeEvent(cars_react(), {
test_vec2 = unique(cars_react()$hp)
if (file.exists("test_list.Rdata")) {
temp = readRDS("test_list.Rdata")
test_list = c(temp, list(test_vec2))
} else {
test_list = list(test_vec2)
}
saveRDS(test_list, file = "test_list.Rdata")
})
# here we access the reactive data with isolate and make it non-reactive, but can update the values through a button click
text_vec <- eventReactive(input$capture, {
isolate(unique(cars_react()$hp))
})
# output of our reactive data as table
output$table <- renderTable({
cars_react()
})
# text output of globally assigned non-reactive vector test_vec3 (not changing!)
output$text <- renderText({
test_vec3
})
# you can capture values of reactives with isolate, but then, they don't change anymore
# text output of isolated formely reactive vector unique(cars_react()$hp (not changing!)
output$text2 <- renderText({
isolate(unique(cars_react()$hp))
})
# text output of new reactive vector (changes when input$capture button is clicked)
output$text3 <- renderText({
text_vec()
})
}
)
I have a function (clawCheck) defined in the file CheckClawback.R which takes three data frames as arguments. In my Shiny app, the user uploads three files which are then read into memory and used as the ClawCheck arguments. In order to save time, I want R to start reading a file into memory as soon as it is uploaded, and not only after the "GO" button is pressed, so that once the button is pressed, the arguments for ClawCheck are already in memory and ready to use.
I'm thinking that I have to use eventReactive expressions within the renderTable statement, since I don't want the files to be re-read every time a user changes some input. To avoid further complication, I assume the input is filled in in order, i.e first "account", then "commpaid", then "termriders". When I run the app and the first input file has been uploaded, there is no progress bar appearing which indicates that my code is not working correctly. Here is my (reduced) code:
library('shiny')
source("CheckClawback.R")
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
fileInput("account", "Account File (.csv)"),
fileInput("commpaid", "CommPaid File (.txt)"),
fileInput("termriders", "TermRiders File (.txt)"),
actionButton("do", "GO!")),
mainPanel(
tableOutput("out_table"))
)
)
server <- function(input, output) {
func <- eventReactive(input$do, {
req(acc)
req(comm)
req(term)
datat <<- clawCheck(acc, comm, term)
})
output$out_table <- renderTable({
eventReactive(input$account, {
withProgress(message = "Preparing Account Data...Please Wait", {
acc <<- read.csv(input$account$datapath, header = TRUE, sep = ",")
})
})
eventReactive(input$commpaid, {
withProgress(message = "Preparing CommPaid Data...Please Wait", {
comm <<- read.table(input$commpaid$datapath, header = TRUE, sep = "\t")
})
})
eventReactive(input$termriders, {
withProgress(message = "Preparing TermRiders Data...Please Wait", {
term <<- read.table(input$termriders$datapath, header = TRUE, sep = "\t")
})
})
withProgress(func(), message = "Loading Output...Please Wait")
datat
})
}
shinyApp(ui = ui, server = server)
Ideally, after a file is uploaded, a progress bar should appear, indicating that it is being processed. If, during this process, a second file is uploaded, a second progress bar should appear, indicating that the second file is being processed etc. Once the actual function call happens, I want the input files to be ready to go.
I am very thankful for any help!
Your use of <<- and withProgress() is wrong. Also, using eventReactive() inside a render*() is wrong. I suggest going through RStudio Shiny tutorials to get help on understanding how reactivity works. Also look at showNotification() instead of withProgress(). For now, here's what you probably need -
server <- function(input, output, session) {
acc <- reactive({
validate(need(input$account), "acc not uploaded")
# use showNotification(); use same approach for other files
read.csv(input$account$datapath, header = TRUE, sep = ",")
# use removeNotification() to remove mesg after file is uploaded
})
comm <- reactive({
validate(need(input$commpaid), "comm not uploaded")
read.table(input$commpaid$datapath, header = TRUE, sep = "\t")
})
term <- reactive({
validate(need(input$termriders), "term not uploaded")
read.table(input$termriders$datapath, header = TRUE, sep = "\t")
})
func <- eventReactive(input$do, {
clawCheck(acc(), comm(), term())
})
output$out_table <- renderTable({
func()
})
}
I'm trying to get a reactiveValue that is depending on a reactive. In the real code (this is a very simplified version), I load a dataset interactively. It changes when pushing the buttons (prevBtn/nextBtn). I need to know the number of rows in the dataset, using this to plot the datapoints with different colors.
The question: Why can't I use the reactive ro() in the reactiveValues function?
For understanding: Why is the error saying "You tried to do something that can only be done from inside a reactive expression or observer.", although ro() is used inside a reactive context.
The error is definitely due to vals(), I already checked the rest.
The code :
library(shiny)
datasets <- list(mtcars, iris, PlantGrowth)
ui <- fluidPage(
mainPanel(
titlePanel("Simplified example"),
tableOutput("cars"),
actionButton("prevBtn", icon = icon("arrow-left"), ""),
actionButton("nextBtn", icon = icon("arrow-right"), ""),
verbatimTextOutput("rows")
)
)
server <- function(input, output) {
output$cars <- renderTable({
head(dat())
})
dat <- reactive({
if (is.null(rv$nr)) {
d <- mtcars
}
else{
d <- datasets[[rv$nr]]
}
})
rv <- reactiveValues(nr = 1)
set_nr <- function(direction) {
rv$nr <- rv$nr + direction
}
observeEvent(input$nextBtn, {
set_nr(1)
})
observeEvent(input$prevBtn, {
set_nr(-1)
})
ro <- reactive({
nrow(dat())
})
output$rows <- renderPrint({
print(paste(as.character(ro()), "rows"))
})
vals <- reactiveValues(needThisForLater = 30 * ro())
}
shinyApp(ui = ui, server = server)
Error in .getReactiveEnvironment()$currentContext() :
Operation not allowed without an active reactive context. (You tried to do something that can only be done from inside a reactive expression or observer.)
I think you want
vals <- reactiveValues(needThisForLater = reactive(30 * ro()))
Not everything in a reactiveValues list is assumed to be reactive. It's also a good place to store constant values. So since it's trying to evaluate the parameter you are passing at run time and you are not calling that line in a reactive environment, you get that error. So by just wrapping it in a call to reactive(), you provide a reactive environment for ro() to be called in.
I am using renderUI to create a "DisplayName" input and I have a reactive function called "ReactiveTest" that uses input$DisplayName. If you run the code below you will see that the "DisplayName" drop down list calls the NameAndID() which in turn calls GetDisplayName() in the global.r file. That call populates the "DisplayName" dropdown list.
BUT when ReactiveTest() tries to access input$DisplayName it says that input$DisplayName is NULL then there seems to be a second call to ReactiveTest() and THEN it sees the input$DisplayName
so when you run the code you will see the timing looks like this:
[1] "Department dropdown list is being returned now"
[1] "Department dropdown list is being returned now"
Listening on http://155.0.0.1:555
[1] "DISPLAY NAME dropdown list is being returned now"
[1] "Now ReactiveTest() tries to access input$DisplayName"
[1] "ReactiveTest() says input$DisplayName Name is NULL" --> why is it NULL? if 2 lines above the dropdown was populated???
[1] "Now ReactiveTest() tries to access input$DisplayName"--> Where is this coming from? Shouldn't there only be 1 call to ReactiveTest()
[1] "ReactiveTest() says input$DisplayName Name is Bob"
I have 3 questions:
(1) Why does ReactiveTest() not see the input$DisplayName after the DisplayName dropdown is called?
(2) Why is there a second call to ReactiveTest()?
(3) How can I make ReactiveTest() see whats in the "DisplayName" dropdown the first call? In my real code I have to test for is.null(input$DisplayName)== TRUE and then not run some code but isn't there a better way?
Here is my code which you can run:
library(shiny)
runApp(list(
ui = basicPage(
sidebarPanel(
selectInput("Department", "Select a department",
choices = as.character(GetDepartments()$Department),
selected = as.character(GetDepartments()$Department[1])),
uiOutput("DisplayName")
),
mainPanel(textOutput("Text") )
),
server = function(input, output, session) {
NameAndID<- reactive({
GetDisplayName(input$Department)
})
output$DisplayName<-renderUI({
Department <- input$Department
selectInput("DisplayName", 'DisplayName:', choices = as.character(NameAndID()$DisplayName), selected =as.character(NameAndID()$DisplayName[1] ))
})
ReactiveTest<- reactive({
print("Now ReactiveTest() tries to access input$DisplayName")
if(is.null(input$DisplayName) == TRUE)
{
print("ReactiveTest() says input$DisplayName Name is NULL")
return("NULL")
}else
{
print(paste0("ReactiveTest() says input$DisplayName Name is ", input$DisplayName))
return(input$DisplayName)
}
})
output$Text <- renderText({
#myData <- GetDisplayName(input$Department)
#code <- as.character(myData[myData$DisplayName == input$DisplayName,2])
return(ReactiveTest())
})
}
))
global.r
GetDepartments<- function(){
df<- data.frame(Department= c("Dept A", "Dept B"), id = c(1,2))
print("Department dropdown list is being returned now")
return(df)
}
GetDisplayName<- function(Dept){
if(Dept == "Dept A")
{
df<- data.frame(DisplayName= c("Bob", "Fred"), id = c(4,6))
print("DISPLAY NAME dropdown list is being returned now")
return(df)
}else
{
df<- data.frame(DisplayName= c("George", "Mary"), id = c(10,20))
print("DISPLAY NAME dropdown list is being returned now")
return(df)
}
}
Your questions are essentially all asking the same thing, why is the function being called twice?
As I mentioned in your previous question, reactive expressions will only run again if they realize something has changed in the input. When you initialize a shiny app with a reactive ui, the values will not be initially loaded (i.e. null values). This has come up before with other shiny questions, such as this one on google groups and a similar one on SO, and the general consensus is that you should have some sort of check in your code (would love to be proven wrong). So your instinct to add a is.null check is correct. This is therefore a nice opportunity to use the validate function. Although this is initialization problem is somewhat annoying, the time taken during initialization should be insignificant.
Here is an example using validate. This however makes it very easy to provider a user friendly error message if somehow a null value is passed and anything passed the validate is not run. More straightforward, in the reactive expression, the initialization only prints and then leaves the function. This type of validation is recommended and documentation can be found here
runApp(list(
ui = basicPage(
sidebarPanel(
selectInput("Department", "Select a department",
choices = as.character(GetDepartments()$Department),
selected = as.character(GetDepartments()$Department[1])),
uiOutput("DisplayName")
),
mainPanel(textOutput("Text") )
),
server = function(input, output, session) {
NameAndID<- reactive({
GetDisplayName(input$Department)
})
output$DisplayName<-renderUI({
Department <- input$Department
selectInput("DisplayName", 'DisplayName:', choices = as.character(NameAndID()$DisplayName), selected =as.character(NameAndID()$DisplayName[1] ))
})
ReactiveTest<- reactive({
print("Now ReactiveTest() tries to access input$DisplayName")
validate(
need(!is.null(input$DisplayName), "ReactiveTest() says input$DisplayName Name is NULL")
)
print(paste0("ReactiveTest() says input$DisplayName Name is ", input$DisplayName))
return(input$DisplayName)
})
output$Text <- renderText({
return(ReactiveTest())
})
}
))