Create a t-test and obtain p-value from csv using shiny - r

Question

I am trying to create a shiny UI to input CSV, perform paired t-test (equal variance) and to generate a heatmap from a sample dataset.
I have been able to generate a UI CSV upload tab, however, I am now struggling with my t-test and p-value tab, I continue to get this error message:
Warning: Error in : evaluation nested too deeply: infinite recursion / options(expressions=)?
90:
shinyServer <- function(input, output, session){
data5<- reactive({
req(input$file1)
data5<-read.csv(input$file1$datapath,
header = input$header,
sep = input$sep,
quote = input$quote)
})
output$contents <- renderTable({
req(input$file1)
if(input$disp == "head") {
return(head(data5()))
}
else {
return(data5())
}
})
####ttests
data1 <- reactive({
data1 <- data.matrix(data5())
})
ctrl <- reactive({
ctrl <- data1()[, c(2:11)]
})
smple <- reactive({
smple <- data1()[, c(12:21)]
})
vector1 <- c(1:10)
pvalue <- c()
pval <- reactive ({
for (i in vector1) {
pvalue[i] <-
t.test(ctrl()[i, ],
smple()[i, ],
paired = FALSE,
var.equal = FALSE)$p.value
}
pvalue
})
signif <- reactive({
sig <- c()
for (n in vector1) {
if (pval()[n] < 0.05) {
sig <- append(sig, n)
}
}
sig
})
genecol <- reactive({
genecol <- data5()[, 1]
})
P.Vals <- reactive({
as.character(P.Vals())
})
data6 <- reactive({
data6 < -data.frame(genecol(), P.Vals())
})
output$pvalue <- renderTable(data6())
}
UI:
library(shiny)
library(shinythemes)
ui <- fluidPage(
####name app
titlePanel("Uploading Files"),
tabsetPanel(
tabPanel("Upload CSV"),
# Sidebar
sidebarLayout(
sidebarPanel(
###input option CSV file
fileInput(
"file1",
"Choose CSV File",
multiple = TRUE,
accept = c("text/csv",
"text/comma-separated-values,text/plain",
".csv")
),
tags$hr(),
###check if CSV has a header
checkboxInput("header", "Header", TRUE),
###format text file into table with separator (comma,semicolon,tab)
radioButtons(
"sep",
"Separator",
choices = c(
Comma = ",",
Semicolon = ";",
Tab = "\t"
),
selected = ","
),
tags$hr(),
####select head of data or all
radioButtons(
"disp",
"Display",
choices = c(Head = "head",
All = "all"),
selected = "head"
)
),
####output panel
mainPanel(# Output: DATA
tableOutput("contents"))
)
),
tabPanel("T-Test",
h4("pvalue"),
tableOutput("pvalue"))
)
I understand this may be complicated but I am a complete beginner, really struggling to get my head round it

Answer 1

Without a reproducible example (see the comments), I am guessing it could be your reactives. I.e.:
data1 <- reactive({
data1 <- data.matrix(data5())
})
A reactive is kinda like a function, as it returns the last value (or whatever is passed with a return statement). In your code, you seem to be reassigning the reactive data1 with a value, within it self. This might not be the case due to scoping, but with the recursive error, this is my first guess.
I suggest you start with editing your reactives to:
data1 <- reactive({
data.matrix(data5())
})
EDIT:
Found it:
P.Vals <- reactive({
as.character(P.Vals())
})
This is most definitely a recursive expression. This is your culprit.