wilcox.test does not work in shiny - r

Question

I am trying to build a 'data explorer' shiny app which contains DataTables, ggplot2 graphs and wilcox.test results. I can't seem to make the wilcox.test to work though.
Outside the shiny app, things work as it should:
dat <- data.frame(outcome=sample(c("died","survived",NA), 20, TRUE),
cntr=sample(c("hospa","hospb"), 20, TRUE),
s=rnorm(20),
t=rnorm(20), stringsAsFactors=FALSE)
wilcox.test(dat$s ~ dat$outcome)
Results:
Wilcoxon rank sum test
data: dat$s by dat$outcome
W = 25, p-value = 0.3301
alternative hypothesis: true location shift is not equal to 0
Within the shiny app, the code below gives an 'Error: grouping factor > must have exactly 2 levels'. (graphs & tables work fine; I have omitted these for clarity).
library(shiny)
library(dplyr)
dat <- data.frame(outcome=sample(c("died","survived",NA), 20, TRUE),
cntr=sample(c("hospa","hospb"), 20, TRUE),
s=rnorm(20),
t=rnorm(20), stringsAsFactors=FALSE)
ui <- navbarPage(
sidebarLayout(
sidebarPanel(
selectInput(inputId = "y",
label = "Y-axis:",
choices = c("s"="s", "t"="t"),
selected = "s"),
selectInput(inputId = "z",
label = "Color by:",
choices = c("outcome", "cntr"),
selected = "outcome")
),
mainPanel(
tabsetPanel(id="tabspanel", type = "tabs",
tabPanel(title = "Wilcox"),
h4(textOutput(outputId = "p")))
)
)
)
server <- function(input, output, session) {
df <- reactive({
data.frame(input$y, input$z)
})
output$p <- renderText({
wilcox.test(df()[,1] ~ df()[,2])
})
}
shinyApp(ui=ui, server=server)
If the code is rewritten:
wilcox.test(dat$s, dat$outcome)
then the error is 'Error: 'x' must be numeric'.
Can someone help?

Answer 1

The issue you are having is that the line
data.frame(input$y, input$z)
gets translated to something like
data.frame("s", "outcome")
which can't be reasonably handeled by wicox.text. You should use the following instead
data.frame(dat[[input$y]], dat[[input$z]])
There were also some other minor issues. See the code code below for a full fix.
library(shiny)
library(dplyr)
dat <- data.frame(outcome=sample(c("died","survived",NA), 20, TRUE),
cntr=sample(c("hospa","hospb"), 20, TRUE),
s=rnorm(20),
t=rnorm(20), stringsAsFactors=FALSE)
ui <- navbarPage(
sidebarLayout(
sidebarPanel(
selectInput(inputId = "y",
label = "Y-axis:",
choices = c("s"="s", "t"="t"),
selected = "s"),
selectInput(inputId = "z",
label = "Color by:",
choices = c("outcome", "cntr"),
selected = "outcome")
),
mainPanel(
tabsetPanel(id="tabspanel", type = "tabs",
tabPanel(title = "Wilcox",
verbatimTextOutput(outputId = "p")))
)
)
)
server <- function(input, output, session) {
df <- reactive({
data.frame(dat[[input$y]], dat[[input$z]])
})
output$p <- renderPrint({
wilcox.test(df()[,1] ~ df()[,2])
})
}
shinyApp(ui=ui, server=server)

Answer 2

Gregor's guess is quite spot on; below snippet from the server codes:
dat_subset <- reactive({
req(input$selected_type)
filter(dat, outcome %in% input$selected_type)
})
output$scatterplot <- renderPlot({
ggplot(data = dat_subset(), aes_string(x = input$x, y = input$y, color = input$z)) + geom_boxplot() + labs()
})
output$nsdtable <- DT::renderDataTable({
DT::datatable(data = dat_subset()[, 1:4],
options = list(pageLength = 10),
rownames = FALSE)
})