Unable to display Shiny output in specified tabs - r

I am trying to make a simple shiny app that takes information from a csv file and produces a table and two graphs. The content appears to be loading correctly but I can not seem to get the output to go within the specified tab, making the output appear cluttered and difficult to read. Any help is appreciated. Thank you in advance
library(ggplot2)
library(plater)
server <- function(input, output) {
output$table1 <- renderTable({
req(input$file1)
df <- read_plate(input$file1$datapath)
if(input$disp == "head") {
return(head(df))
}
else {
return(df)
}
data <- reactive({
read_plate(input$file1$datapath)
})
})
{output$Plot1 <- renderPlot({
req(input$file1)
df <- read_plate(input$file1$datapath)
ggplot(df, aes(x=Column, y=Row, size = 20, color = "variabley")) + geom_point()
})
}
output$vx <- renderUI({
req(input$file1)
df <- read_plate(input$file1$datapath)
selectInput("variablex", "Select the (X) Variable", choices = names(df))
})
output$vy <- renderUI({
req(input$file1)
df <- read_plate(input$file1$datapath)
selectInput("variabley", "Select the (y) Variable", choices = names(df))
})
output$p <- renderPlot({
req(input$file1)
df <- read_plate(input$file1$datapath)
ggplot(df, aes(input$variablex, input$variabley, size = 20)) + geom_point()
})
}
ui <- fluidPage(
titlePanel("Enrichment Analysis"),
sidebarLayout(
sidebarPanel(
fileInput("file1", "Choose CSV File",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
tags$hr(),
# Input: Checkbox if file has header ----
checkboxInput("header", "Header", TRUE),
# Input: Select separator ----
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
# Input: Select quotes ----
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"'),
#Checkbox
# Horizontal line ----
tags$hr(),
# Input: Select number of rows to display ----
radioButtons("disp", "Display",
choices = c(Head = "head",
All = "all"),
selected = "head")
),
mainPanel(
tabsetPanel(type = "tab",
tabPanel("Plot", fluid = TRUE,
sidebarLayout(
sidebarPanel(selectInput("colm", "Variable", choices = names(df), selected = "")),
mainPanel(
plotOutput("Plot1")
)
)
),
tabPanel("Plate"),
sidebarPanel(
uiOutput("vx"),
uiOutput("vy"),
mainPanel(plotOutput("p", width = "70%"))
),
tabPanel("Comparison"),
tabPanel("Table")),
tableOutput("table1")
)
)
)
shinyApp(ui, server )

Related

Make selectInput choices reactive between datasets

I want to update one of my selectInputs, "variable" with a reactive list of countries that will change depending on the dataset that is selected in another selectInput, "Databases". I want the default list of choices to be the "Home File" dataset that is loaded when the app runs but I want to have the option of switching to an uploaded file. The files I plan to upload will all have the list of countries under the "Countries" column to match the home_df column. Ideally the list will refresh anytime the dataset is switched.
So far I have tried this but cant seem to return the values I want:
Values <- c(145540,145560, 157247, 145566)
Countries <- c(US, Canada, Ireland, Spain)
Zipcodes <- c(145592, 145560, 145566, NA)
home_df <- data.frame(Values , Countries , Zipcodes )
ui <- fluidPage(
tabPanel(
"first_plot",
tabsetPanel(
id = "firstPanel",
type = "tabs",
tabPanel("File Upload",
# Sidebar layout with input and output definitions ----
sidebarLayout(
# Sidebar panel for inputs ----
sidebarPanel(
# Input: Select a file ----
fileInput(
"file1",
"Choose CSV File",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")
),
# Horizontal line ----
tags$hr(),
# Input: Checkbox if file has header ----
checkboxInput("header", "Header", TRUE),
# Input: Select separator ----
radioButtons(
"sep",
"Separator",
choices = c(
Comma = ",",
Semicolon = ";",
Tab = "\t"
),
selected = ","
),
# Input: Select quotes ----
radioButtons(
"quote",
"Quote",
choices = c(
None = "",
"Double Quote" = '"',
"Single Quote" = "'"
),
selected = '"'
),
# Horizontal line ----
tags$hr(),
# Input: Select number of rows to display ----
radioButtons(
"disp",
"Display",
choices = c(Head = "head",
All = "all"),
selected = "head"
)
),
mainPanel(# Output: Data file ----
tableOutput("contents"))
)),
tabPanel("first_plot",
uiOutput("box"))
server <- function(input, output, session) {
my_data <- reactive({
inFile <- input$file1
req(inFile)
# when reading semicolon separated files,
# having a comma separator causes `read.csv` to error
tryCatch({
df_x <<- read.csv(
inFile$datapath,
header = input$header,
sep = input$sep,
quote = input$quote
)
},
error = function(e) {
# return a safeError if a parsing error occurs
stop(safeError(e))
})
if (input$disp == "head") {
return(head(df_x))
}
else {
return(df_x)
}
})
}
datasetInput <- reactiveValues(
if (input$exp_pr_box == "Home File"){
dataset <- home_df
}
else if (input$exp_pr_box == "Uploaded DB"){
dataset <- my_data()
}
return(dataset)
)
md <- reactiveValues(
list = datasetInput$Countries
)
observeEvent(datasetInput(),
updateSelectInput(session, "variable", choices=md()))
output$box <- renderUI({
tabPanel(
"first_plot",
sidebarPanel(
selectInput(
"exp_pr_box",
"Database",
choices = c("Home File", "Uploaded DB")
), ----
selectInput("variable", "Selection:", choices=NULL, selected = NULL
)
)
),
mainPanel(
h3("plot title", align = "center"),
plotlyOutput("plot", height = '1000px', width = "100%")
)
)
})
output$contents <- renderTable({
my_data()
})
output$plot <- renderPlotly(
ggplot(dx) +
geom_boxplot(col = c("#69b3a2", "red")) +
geom_line(data = dx, aes(group = paired), color =
"grey"))
shinyApp(ui, server)
I was able to solve the issue with the help of this post (R Shiny - How to update a dependent reactive selectInput before updating dependent reactive plot)
And by storing the list in the reactive. For some reason using the names function as was done in the example did not output the list for me but worked after removing it
md <- reactive({
my_list = input_dataset()
})
observeEvent(input$exp_pr_box, {
freezeReactiveValue(input, "variable")
updateSelectInput(session = session, inputId = "variable", choices = unique(str_to_title(md())))
})

R Shiny: read data file, get user to select variable, plot with ggplot

As stated in the title, I'm trying to use Shiny in R to create a program that reads a csv file uploaded by the user, after which the user can select a variable from that file to view a plot that is plotted by ggplot. I'm trying to achieve this over two tabs, the first tab will read the file and the second tab will get the user to select the variable to view the plot.
My codes are as below. Currently, I am able to successfully read the user's file but I am not able to plot based on the variable selected (I currently only have 1 variable "Location" for demo). (HomeWTaxAmt is the y variable to plot against).
library(shiny)
library(ggplot2)
library(data.table)
library(RColorBrewer)
options(scipen=1000)
ui <- fluidPage(
navbarPage("User Interface:",tabPanel("Upload",
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput("file1", "Choose CSV File",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
tags$hr(),
checkboxInput("header", "Header", TRUE),
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
tags$hr(),
radioButtons("disp", "Display",
choices = c(Head = "head",
All = "all"),
selected = "head"),
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"')),
mainPanel(
verbatimTextOutput("summary"),
tableOutput("contents")
))),
tabPanel("Graphing",
titlePanel("Plotting Graphs"),
sidebarLayout(
sidebarPanel(
selectInput("variable", "Variable:",
list("Location"))),
mainPanel(
h3(textOutput("caption")),
plotOutput("ggplot")
)
))
))
server <- function(input, output) {
output$contents <- renderTable({
req(input$file1)
library(data.table)
data <- fread(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
if(input$disp == "head") {
return(head(data))
}
else {
return(data)
}
})
output$summary <- renderPrint({
summary(data)
})
formulaText <- reactive(function() {
paste("HomeWTaxAmt ~", input$variable)
})
output$caption <- renderText(function() {
formulaText()
})
output$ggplot <- renderPlot(function() {
data <- fread(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
if(is.null(data)) return(NULL)
# check for the input variable
ggplot(data, aes(x=reorder(factor(data[input$variable]), -abs(HomeWTaxAmt), function(x){sum(x)}),
weight = abs(HomeWTaxAmt), fill = factor(data[input$variable]))) + geom_bar(show.legend=FALSE) + xlab(input$variable) +
scale_fill_manual(values=brewer.pal(n = 12, name = "Paired"))
})
}
shinyApp(ui, server)
As I did not have access to your exact .csv files I had to make some adjustments to the plotting command, but I'm pretty sure you can go from there and get it to work with your data. Please note that not loading a .csv file now gives you errors on the first tab, which dissapear as soon as data is loaded. You might want to use some ifelse switches here to ensure the end-user doesn't have to see these R-errors.
Here's the code that plots a plot as intended based on some sample data I had:
library(shiny)
library(ggplot2)
library(data.table)
library(RColorBrewer)
options(scipen=1000)
#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# I didn't change anything in this section
ui <- fluidPage(
navbarPage("User Interface:",tabPanel("Upload",
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput("file1", "Choose CSV File",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
tags$hr(),
checkboxInput("header", "Header", TRUE),
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
tags$hr(),
radioButtons("disp", "Display",
choices = c(Head = "head",
All = "all"),
selected = "head"),
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"')),
mainPanel(
verbatimTextOutput("summary"),
tableOutput("contents")
))),
tabPanel("Graphing",
titlePanel("Plotting Graphs"),
sidebarLayout(
sidebarPanel(
selectInput("variable", "Variable:",
list("Location"))),
mainPanel(
h3(textOutput("caption")),
plotOutput("ggplot")
)
))
))
#XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
server <- function(input, output, session) { # make sure to include "session" here, in order to update your inputs later
# create an reactive upload to access your data more quickly and easily
reactive_data <- reactive({
print(input$file1$datapath)
data <- fread(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
return(data)
})
# preview
# no library(data.table) required here, as its already loaded at the beginning of the script)
output$contents <- renderTable({
# load your data
data <- reactive_data()
if(input$disp == "head") {
return(head(data))
}
else {
return(data)
}
})
output$summary <- renderPrint({
summary(reactive_data())
})
formulaText <- reactive({ # no need for function() here
paste("HomeWTaxAmt ~", input$variable)
})
output$caption <- renderText({
formulaText()
})
output$ggplot <- renderPlot({
# load your data
data <- reactive_data()
# to only plot when data is not NULL, make sure to include the plotting command in the if-else statement
# no data
if(is.null(data)){
return(NULL)
}else{
# data
# update your selectInput first, so that all the variables match your .csv headers
updateSelectInput(session, "variable",
choices = colnames(data),
selected = input$variable) # this keeps the input on the last thing selected on tab-change
# check for the input variable
# I used aes_string here so that indexing the colnames works
# you'll have to adjust the plotting command to your needs as my .csv files aren't the same as yours
plot <- ggplot(data, aes_string(x=colnames(data)[colnames(data) == input$variable], colnames(data)[length(colnames(data))]))+
geom_bar(stat="identity")
# Display your plot
print(plot)
}
})
}
shinyApp(ui, server)
Modified your code a bit and i hope it helps you.
library(shiny)
library(ggplot2)
ui <- fluidPage(
navbarPage("User Interface:",tabPanel("Upload",
titlePanel("Uploading Files"),
sidebarLayout(
sidebarPanel(
fileInput("file1", "Choose CSV File",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
tags$hr(),
checkboxInput("header", "Header", TRUE),
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
tags$hr(),
radioButtons("disp", "Display",
choices = c(Head = "head",
All = "all"),
selected = "head"),
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"')),
mainPanel(
verbatimTextOutput("summary"),
tableOutput("contents")
))),
tabPanel("Graphing",
titlePanel("Plotting Graphs"),
sidebarLayout(
sidebarPanel( uiOutput("variable_x"),
uiOutput("variable_y")),
mainPanel(
h3(textOutput("caption")),
plotOutput("plot")
)
))
))
server <- function(input, output, session) {
onSessionEnded(stopApp)
data <- reactive({
req(input$file1)
df <- read.csv(input$file1$datapath, header = input$header, sep = input$sep, quote = input$quote)
return(df)
})
output$contents <- renderTable({
if (input$disp == "head") {
return(head(data()))
}
else {
return(data())
}
})
output$summary <- renderPrint({
summary(data())
})
output$variable_x <- renderUI({
selectInput("variableNames_x", label = "Variable_X", choices = names(data()))
})
output$variable_y <- renderUI({
selectInput("variableNames_y", label = "Variable_Y", choices = names(data()) )
})
dat <- reactive({
test <- data.frame(data()[[input$variableNames_x]], data()[[input$variableNames_y]])
colnames(test) <- c("X", "Y")
return(test)
})
output$plot <- renderPlot({
if (is.null(data)) { return(NULL)
} else {
ggplot(dat(),aes(x = X,y = Y)) + geom_point(colour = 'red',height = 400,width = 600) +
labs(y = input$variableNames_y,
x = input$variableNames_x,
title = "ggplot")
}
})
}
shinyApp(ui, server)
Note : I have changed your ggplot function but you can change as per your requirement.

Passing on data and input within a shiny app

I was trying to simplify my shiny app. However, as much as I try it is not working, as I would like it to.
My Idea was to load data to the app, perform some analyses and return intermediate results to the user. At the moment I have to load the data, choose the right columns etc. for each output I am generating:
ui <- shinyServer(
fluidPage(
tabsetPanel(
tabPanel("Data upload",
titlePanel("Data upload"),
sidebarLayout(
sidebarPanel(
fileInput("file1", "Choose CSV File",multiple = TRUE, accept = c("text/csv","text/comma-separated-values,text/plain",".csv")),
tags$hr(),
checkboxInput("header", "Header", TRUE), radioButtons("sep", "Separator", choices = c(Comma = ",", Semicolon = ";",Tab = "\t"), selected = ","),
tags$hr(),
checkboxInput("disp", "Display",TRUE),
tags$hr(),
uiOutput("choose_first_column"),
uiOutput("choose_second_column"),
br()
),
mainPanel(
tableOutput("contents"),
tags$hr(),
tableOutput("tab")
)
)
),
tabPanel("2","2"
)
)
)
)
server <- shinyServer(
function(input, output) {
observe({
req(input$file1)
df <- read.csv(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
output$contents <- renderTable({
(head(df))})
output$choose_first_column <- renderUI({
colnames <- names(df)
selectInput("column_1", "Choose Date column",
choices = colnames,
selected = colnames)})
output$choose_second_column <- renderUI({
colnames <- names(df)
selectInput("column_2", "Choose Variable column",
choices = colnames,
selected = colnames)})
output$tab <- renderTable({
req(input$file1)
df2 <- read.csv(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
df2 <- df2[, c(input$column_1,input$column_2), drop = FALSE]
return(head(df2))})
})
})
runApp(list(ui = ui, server = server))
It works, but as I usually have many data and I want to perform a couple of analyses, it is gets quite time-consuming to load and process the data for each “output content”.
Is there a way to avoid this? Could I for example load the data and choose the right columns globaly, as in the second example? (I crossed out the lines where the error occurs)
ui <- shinyServer(
fluidPage(
tabsetPanel(
tabPanel("Data upload",
titlePanel("Data upload"),
sidebarLayout(
sidebarPanel(
fileInput("file1", "Choose CSV File",multiple = TRUE, accept = c("text/csv","text/comma-separated-values,text/plain",".csv")),
tags$hr(),
checkboxInput("header", "Header", TRUE), radioButtons("sep", "Separator", choices = c(Comma = ",", Semicolon = ";",Tab = "\t"), selected = ","),
tags$hr(),
checkboxInput("disp", "Display",TRUE),
tags$hr(),
uiOutput("choose_first_column"),
uiOutput("choose_second_column"),
br()
),
mainPanel(
tableOutput("contents"),
tags$hr(),
tableOutput("tab")
)
)
),
tabPanel("2","2"
)
)
)
)
server <- shinyServer(
function(input, output) {
observe({
req(input$file1)
df <- read.csv(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
output$contents <- renderTable({
(head(df))})
output$choose_first_column <- renderUI({
colnames <- names(df)
selectInput("column_1", "Choose Date column",
choices = colnames,
selected = colnames)})
output$choose_second_column <- renderUI({
colnames <- names(df)
selectInput("column_2", "Choose Variable column",
choices = colnames,
selected = colnames)})
# df <- df[, c(input$column_1,input$column_2), drop = FALSE]
#
# output$tab <- renderTable({
# (head(df))})
})
})
runApp(list(ui = ui, server = server))
Input data example:
date time level
01.01.2000 00:00:00 0.3724
01.01.2000 01:00:00 0.192
01.01.2000 02:00:00 -0.0252
I would appreciate any help!
Aishe
From what I've understood, you are getting an error because the dataframe df that you have defined is not reactive. You should make it reactive as it will change every time the user selects input columns.
Refer this to read about reactivity. Change the deleted portion of your code to this:
df.selected.columns <- df[c(input$column_1,input$column_2)]
output$tab <- renderTable({
(head(df.selected.columns()))
})

Render and download data table in Rshiny app

I am unable to render a data table and allow users to download that data table with a shiny application. Here is my MWE
UI:
ui <- fluidPage(
# Application title
titlePanel("Tool v0.03"),
# Sidebar with a slider input for number of bins
sidebarLayout(
sidebarPanel(
fileInput("dataset", "Choose CSV File",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
helpText(em("Note:Select all the inputs and click on button as given below to exectute the app")),
checkboxInput("header", "Header", TRUE),
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
selectInput("select", "Select columns to display", c('col1', 'col2'), multiple = TRUE),
actionButton("update", "Update Data set", class = "btn-primary",style='padding:4px; font-size:120%')
),
mainPanel(
tabsetPanel(type = "tabs",
tabPanel(h2("Random Stratified Sample"), DT::dataTableOutput('out.Sample'),
fluidRow(downloadButton('SampleDownload', "Download sample data"))) # in a tabitem)
)
)
)
)
Server:
server <- function(session, input, output) {
data <- reactive({
req(input$dataset)
Cleaning_Fun(read.csv(input$dataset$datapath, header = input$header,sep =
input$sep))
})
filtereddata <- eventReactive({
input$update
data()
}, {
req(data())
if(is.null(input$select) || input$select == "")
data() else
data()[, colnames(data()) %in% input$select]
})
observeEvent(data(), {
updateSelectInput(session, "select", choices=colnames(data()))
})
output$out.Sample <-
DT::renderDataTable(DT::datatable((filtereddata())
))
output$SampleDownload <- downloadHandler(
filename = function() {
paste('Sample_data-', Sys.Date(), '.csv', sep = '')
},
content = function(file){
write.csv(filtereddata()[input[["SampleData_rows_all"]], ],file)
}
)
}
This example allows the user to render and download a dataset that they have uploaded. Unfortunately the file only contains the header of the data table. Unsure where this is going wrong but, any help appreciated
Thanks,
John

how to show some widgets based on the selection from one widget in shiny app

below is a shiny app to upload a rda or csv file. What I need is only show the checkboxinput and radiobutton widgets only when csv is selected as the file type in the selectinput. When rda is selected, do not show those widgets.
library(shiny)
library(DT)
##---------------------------------------------------------------
## ui
##---------------------------------------------------------------
ui <- fluidPage(
sidebarLayout(
sidebarPanel(
# select a file type
selectInput('filetype', label = h5(strong('Please select a file type')),
choices = c('rda', 'csv'),
selected = 'rda'),
# Input: Select a file ----
fileInput("file1", "Choose a file",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")),
tags$hr(),
# Input: Checkbox if file has header ----
checkboxInput("header", "Header", TRUE),
# Input: Select separator ----
radioButtons("sep", "Separator",
choices = c(Comma = ",",
Semicolon = ";",
Tab = "\t"),
selected = ","),
# Input: Select quotes ----
radioButtons("quote", "Quote",
choices = c(None = "",
"Double Quote" = '"',
"Single Quote" = "'"),
selected = '"')
),
#------------------------------Main Panel--------------------
mainPanel(
DT::dataTableOutput("data.table")
)
)
)
##---------------------------------------------------------------------
# server
##---------------------------------------------------------------------
options(shiny.maxRequestSize=30*1024^2)
server <- function(input, output, session) {
dt <- reactive ({
if (input$filetype %in% 'rda') {
load (input$file1$datapath)
df
} else {
read.csv(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
}
})
output$data.table <- DT::renderDataTable({
req(input$file1)
DT::datatable(dt(),
options = list(orderClasses = TRUE,
lengthMenu = c(5, 10, 20), pageLength = 5))
})
}
runApp(shinyApp(ui=ui, server=server))
Really appreciate it if anyone can help me with that. I have no clue how to achieve that.
Here's a sample of how to do build a dynamic UI that will only show the radio buttons if the file type selected is 'csv'. Refer to https://shiny.rstudio.com/articles/dynamic-ui.html for more.
library(shiny)
ui <- fluidPage(
selectInput(
"select",
label = "File Type",
choices = list("csv", "rda"),
selected = c("csv")
),
conditionalPanel(
condition = "input.select == 'csv'",
radioButtons(
"radio",
label = "Separator",
choices = list("commas", "tabs", "spaces")
)
)
)
server <- function(input, output, session) {
}
shinyApp(ui, server)

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