## MAIN FUNCTION
function(input, output, session) {
# input data (with default)
values <- reactiveValues(data_primary = if ("startData" %in% names(.GlobalEnv)) startData else ExampleData.DeValues$CA1,
data_secondary = setNames(as.data.frame(matrix(NA_real_, nrow = 5, ncol = 2)), c("x", "y")),
data = NULL,
args = NULL)
session$onSessionEnded(function() {
stopApp()
})
# check and read in file (DATA SET 1)
observeEvent(input$file1, {
inFile<- input$file1
if(is.null(inFile))
return(NULL) # if no file was uploaded return NULL
values$data_primary <- fread(file = inFile$datapath, data.table = FALSE) # inFile[1] contains filepath
})
# check and read in file (DATA SET 2)
observeEvent(input$file2, {
inFile<- input$file2
if(is.null(inFile))
return(NULL) # if no file was uploaded return NULL
values$data_secondary <- fread(file = inFile$datapath, data.table = FALSE) # inFile[1] contains filepath
})
### GET DATA SETS
observe({
### GET DATA
data <- list(values$data_primary, values$data_secondary)
data <- lapply(data, function(x) {
x_tmp <- x[complete.cases(x), ]
if (nrow(x_tmp) == 0) return(NULL)
else return(x_tmp)
})
data <- data[!sapply(data, is.null)]
data <- lapply(data, function(x) setNames(x, c("Dose", "Error")))
values$data <- data
})
output$table_in_primary <- renderRHandsontable({
rhandsontable(values$data_primary,
height = 300,
colHeaders = c("Dose", "Error"),
rowHeaders = NULL)
})
observeEvent(input$table_in_primary, {
# Workaround for rhandsontable issue #138
# https://github.com/jrowen/rhandsontable/issues/138
df_tmp <- input$table_in_primary
row_names <- as.list(as.character(seq_len(length(df_tmp$data))))
df_tmp$params$rRowHeaders <- row_names
df_tmp$params$rowHeaders <- row_names
df_tmp$params$rDataDim <- as.list(c(length(row_names),
length(df_tmp$params$columns)))
if (df_tmp$changes$event == "afterRemoveRow")
df_tmp$changes$event <- "afterChange"
if (!is.null(hot_to_r(df_tmp)))
values$data_primary <- hot_to_r(df_tmp)
})
output$table_in_secondary <- renderRHandsontable({
rhandsontable(values$data_secondary,
height = 300,
colHeaders = c("Dose", "Error"),
rowHeaders = NULL)
})
observeEvent(input$table_in_secondary, {
# Workaround for rhandsontable issue #138
# https://github.com/jrowen/rhandsontable/issues/138
df_tmp <- input$table_in_secondary
row_names <- as.list(as.character(seq_len(length(df_tmp$data))))
df_tmp$params$rRowHeaders <- row_names
df_tmp$params$rowHeaders <- row_names
df_tmp$params$rDataDim <- as.list(c(length(row_names),
length(df_tmp$params$columns)))
if (df_tmp$changes$event == "afterRemoveRow")
df_tmp$changes$event <- "afterChange"
if (!is.null(hot_to_r(df_tmp)))
values$data_secondary <- hot_to_r(df_tmp)
})
# dynamically inject sliderInput for x-axis range
output$xlim<- renderUI({
data <- do.call(rbind, values$data)
sliderInput(inputId = "xlim",
label = "Range x-axis",
min = min(data[,1])*0.25,
max = max(data[,1])*1.75,
value = c(min(data[,1])*0.9, max(data[,1])*1.1))
})## EndOf::renderUI()
# dynamically inject sliderInput for KDE bandwidth
output$bw<- renderUI({
data <- do.call(rbind, values$data)
sliderInput(inputId = "bw",
label = "KDE bandwidth",
min = bw.nrd0(data[,1])/4,
max = bw.nrd0(data[,1])*4,
value = bw.nrd0(data[,1]))
})## EndOf::renderUI()
observe({
# make sure that input panels are registered on non-active tabs.
# by default tabs are suspended and input variables are hence
# not available
outputOptions(x = output, name = "xlim", suspendWhenHidden = FALSE)
outputOptions(x = output, name = "bw", suspendWhenHidden = FALSE)
# refresh plot on button press
input$refresh
# check if any summary stats are activated, else NA
summary <- if (input$summary) input$stats else ""
logx <- ifelse(input$logx, "x", "")
# if custom datapoint color get RGB code from separate input panel
color <- ifelse(input$color == "custom", input$rgb, input$color)
# if custom datapoint color get RGB code from separate input panel
if(!all(is.na(unlist(values$data_secondary)))) {
color2 <- ifelse(input$color2 == "custom", input$rgb2, input$color2)
} else {
color2<- adjustcolor("white", alpha.f = 0)
}
values$args <- list(
data = values$data,
cex = input$cex,
log = logx,
xlab = input$xlab,
ylab = c(input$ylab1, input$ylab2),
main = input$main,
values.cumulative = input$cumulative,
na.rm = TRUE,
rug = input$rug,
boxplot = input$boxplot,
summary = summary,
summary.pos = input$sumpos,
summary.method = input$summary.method,
bw = input$bw,
xlim = input$xlim,
col = c(color, color2))
})
output$main_plot <- renderPlot({
# validate(need()) makes sure that all data are available to
# renderUI({}) before plotting and will wait until there
validate(
need(expr = input$xlim, message = ''),
need(expr = input$bw, message = 'Waiting for data... Please wait!')
)
do.call(plot_KDE, args = values$args)
})##EndOf::renderPlot({})
observe({
# nested renderText({}) for code output on "R plot code" tab
code.output <- callModule(RLumShiny:::printCode, "printCode", n_input = 2,
fun = "plot_KDE(data,", args = values$args)
output$plotCode<- renderText({
code.output
})##EndOf::renderText({})
callModule(RLumShiny:::exportCodeHandler, "export", code = code.output)
callModule(RLumShiny:::exportPlotHandler, "export", fun = "plot_KDE", args = values$args)
})
# renderTable() that prints the data to the second tab
output$dataset<- renderDataTable(
options = list(pageLength = 10, autoWidth = FALSE),
callback = "function(table) {
table.on('click.dt', 'tr', function() {
$(this).toggleClass('selected');
Shiny.onInputChange('rows',
table.rows('.selected').values$data.toArray());
});
}",
{
data <- values$data[[1]]
colnames(data) <- c("De","De error")
data
})##EndOf::renterTable()
# renderTable() that prints the secondary data to the second tab
output$dataset2<- renderDataTable(
options = list(pageLength = 10, autoWidth = FALSE),
callback = "function(table) {
table.on('click.dt', 'tr', function() {
$(this).toggleClass('selected');
Shiny.onInputChange('rows',
table.rows('.selected').values$data.toArray());
});
}",
{
if(!all(is.na(unlist(values$data_secondary)))) {
data <- values$data[[2]]
colnames(data) <- c("De","De error")
data
} else {
}
})##EndOf::renterTable()
# renderTable() to print the results of the
# central age model (CAM)
output$CAM<- renderDataTable(
options = list(pageLength = 10, autoWidth = FALSE),
{
data <- values$data
t<- as.data.frame(matrix(nrow = length(data), ncol = 7))
colnames(t)<- c("Data set","n", "log data", "Central dose", "SE abs.", "OD (%)", "OD error (%)")
res<- lapply(data, function(x) { calc_CentralDose(x, verbose = FALSE, plot = FALSE) })
for(i in 1:length(res)) {
t[i,1]<- ifelse(i==1,"pimary","secondary")
t[i,2]<- length(res[[i]]@data$data[,1])
t[i,3]<- res[[i]]@data$args$log
t[i,4:7]<- round(res[[i]]@data$summary[1:4],2)
}
t
})##EndOf::renterTable()
}##EndOf::shinyServer(function(input, output)
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