R Shiny Dashboard - Loading Scripts using source('file.R') - r

Introduction
I have created an R shiny dashboard app that is quickly getting quite complex. I have over 1300 lines of code all sitting in app.R and it works. I'm using RStudio.
My application has a sidebar and tabs and rather than using modules I dynamically grab the siderbar and tab IDs to generate a unique identifier when plotting graphs etc.
I'm trying to reorganise it to be more manageable and split it into tasks for other programmers but I'm running into errors.
Working Code
My original code has a number of library statements and sets the working directory to the code location.
rm(list = ls())
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
getwd()
I then have a range of functions that sit outside the ui/server functions so are only loaded once (not reactive). These are all called from within the server by setting the reactive values and calling the functions from within something like a renderPlot. Some of them are nested, so a function in server calls a function just in regular app.R which in turn calls another one. Eg.
# Start of month calculation
som <- function(x) {
toReturn <- as.Date(format(x, "%Y-%m-01"))
return(toReturn)
}
start_fc <- function(){
fc_start_date <- som(today())
return(fc_start_date)
}
then in server something like this (code incomplete)
server <- function(input, output, session) {
RV <- reactiveValues()
observe({
RV$selection <- input[[input$sidebar]]
# cat("Selected:",RV$selection,"\r")
})
.......
cat(paste0("modelType: ",input[[paste0(RV$selection,"-modeltype")]]," \n"))
vline1 <- decimal_date(start_pred(input[[paste0(RV$selection,"-modeltype")]],input[[paste0(RV$selection,"-modelrange")]][1]))
vline2 <- decimal_date(start_fc())
.......
Problem Code
So now when I take all my functions and put them into different .R files I get errors indicating the functions haven't been loaded. If I load the source files by highlighting them and Alt-Enter running them so they are loaded into memory then click on Run App the code works. But if I rely on Run App to load those source files, and the functions within them, the functions can't be found.
source('./functionsGeneral.R')
source('./functionsQuote.R')
source('./functionsNewBusiness.R')
source('./ui.R')
source('./server.R')
shinyApp(ui, server)
where ui.R is
source('./header.R')
source('./sidebar.R')
source('./body.R')
source('./functionsUI.R')
ui <- dashboardPage(
header,
sidebar,
body
)
Finally the questions
In what order does R Shiny Dashboard run the code. Why does it fail when I put the exact same inline code into another file and reference it with source('./functions.R')? Does it not load into memory during a shiny app session? What am I missing?
Any help on this would be greatly appreciated.
Thanks,
Travis

Ok I've discovered the easiest way is to create a subfolder called R and to place the preload code into that folder. From shiny version 1.5 all this code in the R folder is loaded first automatically.

Related

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)
}

How can I make variables in a Shiny app acccessible to external R scripts deployed with the app?

I am relatively new to programming/R/Shiny. I have a network of R scripts that take in data, transform it, and produce figures that are output to a PDF. I have been using this for some time now. I now need to transfer that process to a Shiny app.
This has been problematic because none of the variables that are present in one script can be used in another.
Is there a "simple" way to make these variables accessible between R scripts ? That would be a much, much simpler solution than trying to transfer the entirety of the code into the app.r file. Any help would be much appreciated. Thanks.
Example code - Here, I would like the user to upload a CSV file and then press a button that runs an R script that modifies and adds to the data, creating two new dataframes. Those two dataframes would then be used in "report.R" to create PDF reports.
library(shiny)
ui <- fluidPage(
fileInput('upload', 'Choose file to upload',
accept ='.csv'
),
actionButton('analyze', 'Analyze the data')
)
server <- function(input, output, session) {
data <- reactive({
req(input$upload)
read.csv <- vroom(input$file$datapath)
})
observeEvent(input$analyze, {
source("analyze.R")
#this transforms data from the csv and produces new dataframes based on the original, call them df1 and df2. df1 and df2 are then used as data in reports generated by:
source("report.R")
}
)
}
shinyApp(ui, server)

Set www location in shiny::shinyApp

I am currently creating a shiny app that gets invoked with shiny::shinyApp via a wrapper function.
startApp <- function(param1, param2, ...){
# in fact, ui and server change based on the parameters
ui <- fluidPage()
server <- function(...){}
runApp(shinyApp(ui, server))
}
When I include resources (like images, videos etc.), I currently use the addResourcePath command and include the resources with a prefix. However, I would like to add a "default resource path" (appDir/www in usual apps). There seems to be no suitable parameter in shinyApp or runApp. Setting the working directory to the resource folder or one level above does not work either.
Here is a short MWE.
## ~/myApp/app.R
library(shiny)
shinyApp(
fluidPage(tags$img(src = "image.gif")),
server <- function(...){}
)
## ~/myApp/www/image.gif
# binary file
If I run the app via RunApp("~/myApp") everything works, but
setwd("~/myApp")
myApp <- shinyApp(source("app.R")$value)
runApp(myApp)
will fail to display the image. Any suggestions are appreciated.
Context
The reason I want to start the app based on an shiny.appobj (an object that represents the app) rather than a file path is, that the latter approach does not work well with passing parameters to an app. Here is a discussion about this topic.
The recommended way of passing parameters to an app that gets invoked by runApp("some/path") is as follows:
startApp <- function(param1, param2, ...) {
.GlobalEnv$.param1 <- param1
.GlobalEnv$.param2 <- param2
.GlobalEnv$.ellipsis <- as.list(...)
on.exit(rm(.param1, .param2, .ellipsis, envir = .GlobalEnv))
runApp("~/myApp")
}
This approach is just ugly IMO and I get warnings when I build the package that contains the app together with the startApp function. Those warnings occur because the package then breaks the recommended scoping model for package development.
In the help documentation in shiny::runApp, it says appDir could be either of the below:
A directory containing server.R, plus, either ui.R or a www directory
that contains the file index.html.
A directory containing app.R.
An .R file containing a Shiny application, ending with an expression
that produces a Shiny app object.
A list with ui and server components.
A Shiny app object created by shinyApp.
When you run via RunApp("~/myApp"), it is a directory containing app.R
If you want to run via a shiny app object created by shinyApp
you can try things like
myapp_obj <- shinyApp(
fluidPage(tags$img(src = "image.gif")),
server <- function(...){}
)
runApp(myapp_obj)
Update
create a script myapp_script.R with
shinyApp(
fluidPage(tags$img(src='image.gif')),
server <- function(...){}
)
and then call runApp("myapp_script.R")

Not able to run external R script from end user local library into Shiny app(shinyapp.io)

UPDATED
I created one shiny app. there end user can run their Function(R Script). I enabled those things over this function(below)
server.R
observeEvent(input$v1,{
inFile <- input$v1
if (is.null(inFile))
return(NULL)
})
ui.R
fileInput('v1', 'End user function only in R script',accept=c('R/ R script','.R'))
above both codes are only small pieces. i want to run my separate R file over browsing Here that codes are not sourced. i want to get that function inside my shiny app and plot in my graph.
My problem is whole things working normally in my local host, I deployed this same app in shinyapp.io after that the end user part is not working(not whole app)
I am stuck with this past three days!
Guys is it possible to do?? Can any one help me??
I hope you Guys understand this. if not sorry!!!
Thanks in advance
I found the answer my self:
Include load() function in server page and get sourced the external file over load button.
inside the server code like this.
load_Rdata <- function(){
if(is.null(input$file)) return(NULL)
inFile <- isolate({ input$file })
source(inFile$datapath)
}
call this function inside the observe event
observeEvent(input$btnLoad,{
load_Rdata()
}) `
UI code like this
fileInput("file", label = "Rdata"),
actionButton(inputId="btnLoad","Load")
get the file over fileInput and source the file using load button to call load_Rdata to source file..

Reading an RData file into Shiny Application

I am working on a shiny app that will read a few RData files in and show tables with the contents. These files are generated by scripts that eventually turns the data into a data frame. They are then saved using the save() function.
Within the shiny application I have three files:
ui.R, server.R, and global.R
I want the files to be read on an interval so they are updated when the files are updated, thus I am using:
reactiveFileReader()
I have followed a few of the instructions I have found online, but I keep getting an error "Error: missing value where TRUE/FALSE is needed". I have tried to simplify this so I am not using:
reactiveFileReader()
functionality and simply loading the file in the server.R (also tried in the global.R file). Again, the
load()
statement is reading in a data frame. I had this working at one point by loading in the file, then assigning the file to a variable and doing an "as.data.table", but that shouldn't matter, this should read in a data frame format just fine. I think this is a scoping issue, but I am not sure. Any help? My code is at:
http://pastebin.com/V01Uw0se
Thanks so much!
Here is a possible solution inspired by this post http://www.r-bloggers.com/safe-loading-of-rdata-files/. The Rdata file is loaded into a new environment which ensures that it will not have unexpected side effect (overwriting existing variables etc). When you click the button, a new random data frame will be generated and then saved to a file. The reactiveFileReader then read the file into a new environment. Lastly we access the first item in the new environment (assuming that the Rdata file contains only one variable which is a data frame) and print it to a table.
library(shiny)
# This function, borrowed from http://www.r-bloggers.com/safe-loading-of-rdata-files/, load the Rdata into a new environment to avoid side effects
LoadToEnvironment <- function(RData, env=new.env()) {
load(RData, env)
return(env)
}
ui <- shinyUI(fluidPage(
titlePanel("Example"),
sidebarLayout(
sidebarPanel(
actionButton("generate", "Click to generate an Rdata file")
),
mainPanel(
tableOutput("table")
)
)
))
server <- shinyServer(function(input, output, session) {
# Click the button to generate a new random data frame and write to file
observeEvent(input$generate, {
sample_dataframe <- data.frame(a=runif(10), b=rnorm(10))
save(sample_dataframe, file="test.Rdata")
rm(sample_dataframe)
})
output$table <- renderTable({
# Use a reactiveFileReader to read the file on change, and load the content into a new environment
env <- reactiveFileReader(1000, session, "test.Rdata", LoadToEnvironment)
# Access the first item in the new environment, assuming that the Rdata contains only 1 item which is a data frame
env()[[names(env())[1]]]
})
})
shinyApp(ui = ui, server = server)
Ok - I figured out how to do what I need to. For my first issue, I wanted the look and feel of 'renderDataTable', but I wanted to pull in a data frame (renderDataTable / dataTableOutput does not allow this, it must be in a table format). In order to do this, I found a handy usage of ReportingTools (from Bioconductor) and how they do it. This allows you to use a data frame directly and still have the HTML table with the sorts, search, pagination, etc.. The info can be found here:
https://bioconductor.org/packages/release/bioc/html/ReportingTools.html
Now, for my second issue - updating the data and table regularly without restarting the app. This turned out to be simple, it just took me some time to figure it out, being new to Shiny. One thing to point out, to keep this example simple, I used renderTable rather than the solution above with the ReportingTools package. I just wanted to keep this example simple. The first thing I did was wrap all of my server.R code (within the shinyServer() function) in an observe({}). Then I used invalidateLater() to tell it to refresh every 5 seconds. Here is the code:
## server.R ##
library(shiny)
library(shinydashboard)
library(DT)
shinyServer(function(input, output, session) {
observe({
invalidateLater(5000,session)
output$PRI1LastPeriodTable <- renderTable({
prioirtyOneIncidentsLastPeriod <- updateILP()
})
})
})
Now, original for the renderTable() portion, I was just calling the object name of the loaded .Rdata file, but I wanted it to be read each time, so I created a function in my global.R file (this could have been in server.R) to load the file. That code is here:
updateILP <- function() {
load(file = "W:/Projects/R/Scripts/ITPOD/itpod/data/prioirtyOneIncidentsLastPeriod.RData", envir = .GlobalEnv)
return(prioirtyOneIncidentsLastPeriod)
}
That's it, nothing else goes in the global.R file. Your ui.R would be however you have it setup, call tableOutout, dataTableOutput, or whatever your rendering method is in the UI. So, what happens is every 5 seconds the renderTable() code is read every 5 seconds, which in turns invokes the function that actually reads the file. I tested this by making changes to the data file, and the shiny app updated without any interaction from me. Works like a charm.
If this is inelegant or is not efficient, please let me know if it can be improved, this was the most straight-forward way I could figure this out. Thanks to everyone for the help and comments!

Resources