updatePickerInput instantly refreshing update - r

Question

I have almosat completed a very basic web app in shiny.
I have it functioning as intended, however I believe I have incorrectly used "updatePickerInput" as the table is rendered as expected, however I am not able to select any options in my two pickers as it seems to continue to instantly refresh. I assume this is because the session is looking for input and then regenerating the output, which includes my picker refresh (so I have causes a cyclical refresh). I may be wrong though.
I have looked up the literature but I am unsure exactly what i have done wrong and what the syntax should be to prevent this from occuring.
Typical input is a .csv matrix with different animals on X-axis row 1 (column names) and Y-axis column 1 (row names) with values between any two animals.
library(shiny)
library(ggplot2)
library(shinyWidgets)
library(DT)
options(shiny.maxRequestSize = 50*1024^2)
# Define UI
ui <- fluidPage(
# Application title
titlePanel("Interactive Relatedness Comparison"),
# Sidebar inputs
sidebarLayout(
mainPanel(dataTableOutput("contents")),
sidebarPanel(
#Upload GRM file
fileInput("file1", "Choose GRM File", accept= c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv")),
#Client can choose sires along x-axis
pickerInput(
inputId = "sireselect",
label = "Select Sires",
choices = "Please Upload GRM",
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE, liveSearch = TRUE),
),
#Client can choose dams along y-axis
pickerInput(
inputId = "damselect",
label = "Select Dams",
choices = "Please Upload GRM",
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE, liveSearch = TRUE),
),
#Show raw values
checkboxInput("relatedness", "Show Values (will reset sorting)", value = FALSE),
)
),
)
server <- function(input, output, session) {
#Output uploaded table as data table
output$contents <- DT::renderDataTable({
rownames = TRUE
inFile <- input$file1
if (is.null(inFile))
return(NULL)
file2 <- read.csv(inFile$datapath)
#shiney data table render was not showing row names correctly, changed to DT
rownames(file2) <- file2[,1]
#Remove first column which is now the rownames
file2 <- file2[-c(1)]
#Update pickers for the row/column names
updatePickerInput(session, inputId = "damselect", choices = rownames(file2), selected = rownames(file2))
updatePickerInput(session, inputId = "sireselect", choices = colnames(file2), selected = colnames(file2))
#Create summarized data table (to be primary view unless raw values selected)
newgrid <- as.data.frame(file2)
#Generate summarised data table
for (irow in 1:nrow(file2)){
for (icol in 1:ncol(file2)){
dig <- file2[irow,icol]
if (dig >= 0.8) {
newgrid[irow,icol] <- "SAME"
} else if (dig >= 0.3) {
newgrid[irow,icol] <- "HIGH"
} else if (dig >= 0.1) {
newgrid[irow,icol] <- "MED"
} else {
newgrid[irow,icol] <- "NOT"
}
}
}
#Check box for raw values or not
if (input$relatedness == TRUE){
return(file2[input$damselect,input$sireselect])
} else {
return(newgrid[input$damselect,input$sireselect])
}
})
}
# Run the application
shinyApp(ui, server)
Any help would ne much appreciated

Answer 1

Read in data and updatePickerInput outside of output$contents might help. Try this
library(shiny)
library(ggplot2)
library(shinyWidgets)
library(DT)
options(shiny.maxRequestSize = 50*1024^2)
# Define UI
ui <- fluidPage(
# Application title
titlePanel("Interactive Relatedness Comparison"),
# Sidebar inputs
sidebarLayout(
mainPanel(DTOutput("contents")),
sidebarPanel(
#Upload GRM file
fileInput("file1", "Choose GRM File", accept= c(
"text/csv",
"text/comma-separated-values,text/plain",
".csv")),
#Client can choose sires along x-axis
pickerInput(
inputId = "sireselect",
label = "Select Sires",
choices = "Please Upload GRM",
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE, liveSearch = TRUE),
),
#Client can choose dams along y-axis
pickerInput(
inputId = "damselect",
label = "Select Dams",
choices = "Please Upload GRM",
multiple = TRUE,
options = pickerOptions(actionsBox = TRUE, liveSearch = TRUE),
),
#Show raw values
checkboxInput("relatedness", "Show Values (will reset sorting)", value = FALSE),
)
)
)
server <- function(input, output, session) {
file3 <- reactive({
rownames = TRUE
inFile <- input$file1
if (is.null(inFile))
return(NULL)
file2 <- read.csv(inFile$datapath)
#shiney data table render was not showing row names correctly, changed to DT
rownames(file2) <- file2[,1]
#Remove first column which is now the rownames
file2 <- file2[-c(1)]
file2
})
observe({
req(file3())
updatePickerInput(session, inputId = "damselect", choices = rownames(file3()), selected = rownames(file3()))
updatePickerInput(session, inputId = "sireselect", choices = colnames(file3()), selected = colnames(file3()))
})
#Output uploaded table as data table
output$contents <- renderDT({
req(file3())
#Create summarized data table (to be primary view unless raw values selected)
newgrid <- as.data.frame(file3())
#Generate summarised data table
for (irow in 1:nrow(file3())){
for (icol in 1:ncol(file3())){
dig <- file3()[irow,icol]
if (dig >= 0.8) {
newgrid[irow,icol] <- "SAME"
} else if (dig >= 0.3) {
newgrid[irow,icol] <- "HIGH"
} else if (dig >= 0.1) {
newgrid[irow,icol] <- "MED"
} else {
newgrid[irow,icol] <- "NOT"
}
}
}
#Check box for raw values or not
if (input$relatedness == TRUE){
return(file3()[input$damselect,input$sireselect])
}else {
return(newgrid[input$damselect,input$sireselect])
}
})
}
# Run the application
shinyApp(ui, server)