Obtain contingecy table based on users input - Rshiny

Question

If I want to obtain the fisher test first I need a contigency table. I can do that for the Arthritis package by simply:

library(vcd)
data(Arthritis)
freq <- as.data.frame.matrix(table(Arthritis$Treatment, Arthritis$Improved))
> freq
        None Some Marked
Placebo   29    7      7
Treated   13    7     21

So I could do for example, a fisher test for:

        Not marked Marked
Placebo   36           7
Treated   20          21

For now, what I want to do in shiny is allow the user to select two categorical variables (Treatment and Improved), and then filter by another one (Gender) and obtain the contingency table.

I could use later this one to obtain the 2x2 frequency. But for now this is what I have:

# Shiny
library(shiny)
library(shinyWidgets)
library(shinyjqui)

# Data
library(vcd)
library(readxl)
library(dplyr)
library(arules) # Discretization

# Plots
library(ggplot2)


not_sel <- "Not Selected"

ui <- fluidPage(
  
  
  titlePanel("Plotter"),
    sidebarPanel(
      fileInput("xlsx_input", "Select XLSX file to import", accept = c(".xlsx")),
      selectInput("num_var_1", "Variable X axis", choices = c(not_sel)),
      selectInput("num_var_2", "Variable Y axis", choices = c(not_sel)),
      selectInput("biomarker", "Select Biomarker", choices = c(not_sel)), uiOutput("factor")
      ),
    mainPanel(
      tabsetPanel(
        tabPanel(
          verbatimTextOutput("test")
        
      )
    )
  )
)



## Server ##

server <- function(input, output){
  
  # Dynamic selection of the data. We allow the user to input the data that they want 
  data_input <- reactive({
    #req(input$xlsx_input)
    #inFile <- input$xlsx_input
    #read_excel(inFile$datapath, 1)
    Arthritis
  })
  
  # We update the choices available for each of the variables
  observeEvent(data_input(),{
    choices <- c(not_sel, names(data_input()))
    updateSelectInput(inputId = "num_var_1", choices = choices)
    updateSelectInput(inputId = "num_var_2", choices = choices)
    updateSelectInput(inputId = "biomarker", choices = choices)
  })
  
  num_var_1 <- eventReactive(input$run_button, input$num_var_1)
  num_var_2 <- eventReactive(input$run_button, input$num_var_2)
  biomarker <- eventReactive(input$run_button, input$biomarker)
  
  output$factor <- renderUI({
    req(input$biomarker, data_input())
    if (input$biomarker != not_sel) {
      b <- unique(data_input()[[input$biomarker]])
      pickerInput(inputId = 'selected_factors',
                  label = 'Select factors',
                  choices = c(b[1:length(b)]), selected=b[1], multiple = TRUE,
                  # choices = c("NONE",b[1:length(b)]), selected="NONE", If we want "NONE" to appear as the first option
                  # multiple = TRUE,  ##  if you wish to select multiple factor values; then deselect NONE
                  options = list(`actions-box` = TRUE)) #options = list(`style` = "btn-warning"))
    }
  })
  
  
  data_stats_discrete <- reactive({
    req(data_input(), input$num_var_1, input$num_var_2, input$biomarker) 
    # We filter by biomarker in case user selected, otherwise data_input() remains the same
    if (input$biomarker != "Not Selected") df <- data_input()[data_input()[[input$biomarker]] %in% input$selected_factors,]
    else df <- data_input()
    df <- as.data.frame.matrix(table(.data[[input$num_var_1]], .data[[input$num_var_2]]))
    df
  })
  
  output$test <- renderPrint(data_stats_discrete())
  
  
}


shinyApp(ui = ui, server = server)

As you can see in this RepEx, no dataframe is being selected in the data_stats_discrete.

Answer 1

Change

df <- as.data.frame.matrix(table(.data[[input$num_var_1]], .data[[input$num_var_2]]))

to

df <- as.data.frame.matrix(table(df[[input$num_var_1]], df[[input$num_var_2]]))