I am building an app that allows the user to upload a data file and then analyse the data using a standard method. The analysis is dependent on one user input parameter which is populated after the file is uploaded.
The process is:
- User uploads .csv file.
- uiOutput() is populated with the unique levels in a variable of the uploaded data.
- User selects one option in the uiOutput()
- User clicks 'Run analysis'.
- Table is shown with results.
- User can download the analysis results table as a .csv.
Step 4 of the analysis should filter the data by the input from step 3.
I used renderUI in the server function to make the choices based on unique names (levels) in a variable of the file uploaded by the user. Instead of selectInput() in the ui, I have used uiOutput, based on previous answers on SO. This allows the input to be populated based on the uploaded data. But this is actually an output of a renderUI. I would like this option to filter the data, but I don't know how to specify this filtering condition.
The code chunk of interest is #### run analysis based on user input ####
library(shiny)
library(shinythemes)
library(shinyWidgets)
library(dplyr)
library(DT)
library(shinyjs)
library(dplyr)
library(tidyr)
library(stringr)
data_example <- structure( # save as .csv and upload to app
list(
site = c("A", "A", "A"),
analyte = c("x", "y",
"z"),
QA = c(4L, 6L, 3L),
A1 = c(2L, 6L, 5L),
A2 = c(1L, 8L,
4L),
A3 = c(8L, 32L, 12L)
),
class = "data.frame",
row.names = c(NA,-3L)
)
#### Define UI for data upload app ####
ui <- fluidPage(theme = shinytheme("flatly"),
# set the theme aesthetic
# App title ----
tags$h3("demo"),
# Sidebar layout with input and output definitions ----
sidebarLayout(
sidebarPanel(
width = 3,
#### conditional panel for surface water QA ######
conditionalPanel(
condition = "input.conditionedPanels == 1",
tags$h4("Load data"),
tags$hr(style = "border-color: black;"),
fileInput(
"file1",
"Import file",
multiple = FALSE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")
),
checkboxInput("header", "The dataset has column names", TRUE),
radioButtons(
"sep",
"How are the columns seperated?*",
choices = c(
Comma = ",",
Semicolon = ";",
Tab = "\t"
),
selected = ",",
inline = TRUE
),
tags$hr(style = "border-color: black;"),
tags$h4("Analysis options"),
checkboxInput("show_sw", label = "Show data", value = TRUE),
uiOutput("select_qa_site"),
actionButton("run_qa", "Run analysis"),
downloadButton("download_qa_sw_table", "Download results")
)
),
#### Main panel (tabs) for displaying outputs ####
mainPanel(
useShinyjs(),
tabsetPanel(
type = "tabs",
tabPanel(
"QA",
br(),
tags$h4("Raw data view"),
tags$hr(style = "border-color: black;"),
dataTableOutput("sw_table"),
br(),
tags$h4("Analysis view"),
tags$hr(style = "border-color: black;"),
dataTableOutput("sw_qa_results_table"),
value = 1
),
id = "conditionedPanels"
)
)
))
server <- function(input, output) {
#### data input for surface water ####
data_input <- reactive({
read.csv(input$file1$datapath,
header = input$header,
sep = input$sep)
})
#### sample site names to choose from and run QA analysis ####
sw_site_names <- reactive({
req(input$file1)
names_sw_data <- colnames(data_input())
names_sw_data[!(colnames(data_input()) %in% c("site",
"analyte",
"QA"))]
})
output$select_qa_site <- renderUI({
# Selecting site names based on variable in uploaded data
selectInput(
"Select_site",
label = h4("Select QA sample site"),
choices = sw_site_names(),
selected = NULL
)
})
#### produce data table for raw data inspection ####
output$sw_table <- renderDataTable({
req(input$file1)
datatable(
data_input(),
rownames = FALSE,
options = list(autoWidth = TRUE, scrollX = TRUE)
)
})
#### show/hide raw data table ####
observeEvent(input$show_sw, {
if (input$show_sw)
show("sw_table")
else
hide("sw_table")
})
#### run analysis based on user input ####
qa_table <- eventReactive(input$run_qa, {
data_input() %>%
gather(sample_location,
value,-c(site, analyte, QA)) %>%
mutate(
absolute_diff = abs(value - QA),
value_mean = (value + QA) / 2,
RPD = round((absolute_diff / value) * 100, 2)
) %>%
filter() # I would like to filter this data based on input from user #
})
#### render results of QA analysis to a table for inspection before downloading ####
output$sw_qa_results_table <- renderDataTable({
req(input$file1)
datatable(
qa_table(),
rownames = FALSE,
options = list(autoWidth = FALSE, scrollX = TRUE)
)
})
}
##### Create Shiny app ####
shinyApp(ui, server)
I could be just over-engineering the code too, so I'm happy for suggestions that achieve the same outcome but use a different approach.
I have searched for a solution on SO and do not think this is a duplicate question but I'm happy to be directed to a solution if it exists already.
Any help is appreciated.
