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server.R
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server <- function(input, output, session) {
reac__uploaded_files <- reactiveValues(dt=data.frame("Filename"=character(0), "Size"=character(0), "Path"=character(0), "Remove"=character(0)))
reac__manual_input <- reactiveValues(el=NULL)
reac__manual_input_names <- reactiveValues(names=list())
observeEvent(input$btn__add_dose, {
new_id <- UUIDgenerate()
reac__manual_input$el <- append(reac__manual_input$el,
list(
fluidRow(
column(4,
numericInput(inputId=paste0("input__manual_dose__", new_id), label=paste0("Dose ", length(reac__manual_input$el) + 1), min=0, max=100000, step=0.0001, value=0)
),
column(4,
numericInput(inputId=paste0("input__manual_reps__", new_id), label=paste0("# Reps"), min=1, max=100, step=1, value=1)
),
column(4,
actionButton(inputId=paste0("btn__remove__", new_id), label=NULL, icon=icon("trash"), lib="glyphicons")
)
)
)
)
reac__manual_input$el <- reac__manual_input$el[!vapply(reac__manual_input$el, is.null, FUN.VALUE=logical(1))]
reac__manual_input_names$names <- append(reac__manual_input_names$names, new_id)
names(reac__manual_input$el) <- reac__manual_input_names$names
for(x in seq_len(length(names(reac__manual_input$el)))){
# fix input labels
updateNumericInput(session, inputId=paste0("input__manual_dose__", names(reac__manual_input$el)[x]), label=paste0("Dose ", x), value=input[[paste0("input__manual_dose__", names(reac__manual_input$el)[x])]])
updateNumericInput(session, inputId=paste0("input__manual_reps__", names(reac__manual_input$el)[x]), label=paste0("# Reps"), value=input[[paste0("input__manual_reps__", names(reac__manual_input$el)[x])]])
}
observeEvent(input[[paste0("btn__remove__", new_id)]], {
reac__manual_input$el <- reac__manual_input$el[names(reac__manual_input$el) != new_id]
reac__manual_input_names$names <- reac__manual_input_names$names[reac__manual_input_names$names != new_id]
for(x in seq_len(length(names(reac__manual_input$el)))){
# fix input labels
updateNumericInput(session, inputId=paste0("input__manual_dose__", names(reac__manual_input$el)[x]), label=paste0("Dose ", x), value=input[[paste0("input__manual_dose__", names(reac__manual_input$el)[x])]])
updateNumericInput(session, inputId=paste0("input__manual_reps__", names(reac__manual_input$el)[x]), label=paste0("# Reps"), value=input[[paste0("input__manual_reps__", names(reac__manual_input$el)[x])]])
}
}, once=TRUE)
output$container__manual_input <- renderUI({
reac__manual_input$el
})
})
observeEvent(input$input__dose_input_type, {
reac__manual_input$el <- NULL
reac__manual_input_names$names <- list()
if(input$input__dose_input_type == "auto") {
if(input$input__output_mode == "edf"){
shinyjs::show("input__auto_edf")
shinyjs::hide("input__auto_supp")
shinyjs::hide("input__manual")
} else if(input$input__output_mode == "supp"){
shinyjs::hide("input__auto_edf")
shinyjs::show("input__auto_supp")
shinyjs::hide("input__manual")
}
} else if(input$input__dose_input_type == "manual") {
shinyjs::hide("input__auto_edf")
shinyjs::hide("input__auto_supp")
shinyjs::show("input__manual")
}
})
observeEvent(input$input__output_mode, {
if(input$input__output_mode == "noedf"){
shinyjs::hide("options__edf")
shinyjs::show("options__noedf")
} else {
shinyjs::show("options__edf")
shinyjs::hide("options__noedf")
if(input$input__output_mode == "edf"){
shinyjs::show("input__dose_input_type")
if(input$input__dose_input_type == "auto") {
if(input$input__output_mode == "edf"){
shinyjs::show("input__auto_edf")
shinyjs::hide("input__auto_supp")
shinyjs::hide("input__manual")
} else if(input$input__output_mode == "supp"){
shinyjs::hide("input__auto_edf")
shinyjs::show("input__auto_supp")
shinyjs::hide("input__manual")
}
} else if(input$input__dose_input_type == "manual") {
shinyjs::hide("input__auto_edf")
shinyjs::hide("input__auto_supp")
shinyjs::show("input__manual")
}
} else if(input$input__output_mode == "supp"){
shinyjs::hide("input__dose_input_type")
shinyjs::hide("input__auto_edf")
shinyjs::show("input__auto_supp")
shinyjs::hide("input__manual")
}
}
})
observeEvent(input$input__sample_file, {
shinyjs::hide("btn__download_zip")
shinyjs::show("file_display")
shinyjs::enable("btn__go")
# Process uploaded files for display
uploaded_files_df <- input$input__sample_file
uploaded_files_df$type <- NULL
uploaded_files_df$size <- lapply(uploaded_files_df$size, function(x) {
size_units <- "KB"
tmp <- as.numeric(x) / 1000
if(tmp > 1000){
size_units <- "MB"
tmp <- as.numeric(x) / 1000000
}
return(paste0(round(tmp, digits=2), size_units))
}) # convert file size to kb/mb
uploaded_files_df$remove <- lapply(seq_len(nrow(uploaded_files_df)), function(x){
as.character(
actionButton(
inputId=paste0("btn__remove_file__", x),
label=NULL,
icon=icon("trash"),
lib="glyphicon",
onclick=paste0("Shiny.setInputValue(\'remove_file\', ", x, ", {priority: 'event'})")
)
)
})
colnames(uploaded_files_df) <- c("Filename", "Size", "Path", "Remove")
reac__uploaded_files$dt <- uploaded_files_df
output$output__uploaded_files <- DT::renderDataTable({
DT::datatable(
uploaded_files_df[, c("Filename", "Size", "Remove")],
caption="Uploaded files",
options=list(dom="t"),
selection="none",
escape=FALSE
)
})
})
observeEvent(input$remove_file, {
reac__uploaded_files$dt <- reac__uploaded_files$dt[(row.names(reac__uploaded_files$dt) != input$remove_file),]
uploaded_files_df <- reac__uploaded_files$dt
if(nrow(uploaded_files_df) < 1){
shinyjs::hide("file_display")
} else {
output$output__uploaded_files <- DT::renderDataTable({
DT::datatable(
uploaded_files_df[, c("Filename", "Size", "Remove")],
caption="Uploaded files",
options=list(dom="t"),
selection="none",
escape=FALSE
)
})
}
})
output$output__file_viz <- renderUI({
h4("Generate data first to view a preview here.")
})
dl_uuid <- reactiveValues(uuid=NULL)
observeEvent(input$btn__go, {
# Hide download button
shinyjs::hide("btn__download_zip")
shinyjs::disable("btn__go")
if(nrow(reac__uploaded_files$dt) < 1){
showNotification("Error: no input files provided.", type="error")
shinyjs::enable("btn__go")
return(FALSE)
}
if(input$input__output_mode != "supp" & nrow(reac__uploaded_files$dt) > 1){
showNotification("Error: multiple input files are not supported in this mode.", type="error")
shinyjs::enable("btn__go")
return(FALSE)
}
# #Check if sufficient samples will be generated
if(input$input__replacement == FALSE){
if(input$input__dose_input_type == "auto"){
if(input$input__output_mode == "edf"){
if(input$input__num_synthetic_samples_pool < (input$input__num_rep_d0 + (input$input__num_rep_nod0 * (input$input__num_treatment_groups- 1)))){
showNotification("Error: not enough samples will be generated to sample without replacement. Either increase the sample pool size or allow sampling with replacement.", type="error")
shinyjs::enable("btn__go")
return(FALSE)
}
} else if(input$input__output_mode == "supp"){
if(input$input__num_synthetic_samples_pool < input$input__num_rep_d0_supp | input$input__num_synthetic_samples_pool < input$input__num_rep_nod0_supp){
showNotification("Error: not enough samples will be generated to sample without replacement. Either increase the sample pool size or allow sampling with replacement.", type="error")
shinyjs::enable("btn__go")
return(FALSE)
}
}
}
}
set_uuid <- UUIDgenerate()
dl_uuid$uuid <- set_uuid
if(Sys.info()["sysname"] == "Windows"){
proc_status_list <- apply(reac__uploaded_files$dt, 1, function(x){
# parse out manual input ids
manual_input_list <- list()
if(input$input__dose_input_type == "manual"){
manual_input_list <- lapply(seq_len(length(names(reac__manual_input$el))), function(x){
list(
dose=input[[paste0("input__manual_dose__", names(reac__manual_input$el)[x])]],
reps=input[[paste0("input__manual_reps__", names(reac__manual_input$el)[x])]]
)
})
names(manual_input_list) <- names(reac__manual_input$el)
# Show error if no dosage levels specified
if(length(manual_input_list) < 1){
showNotification("Error: no dosage levels specified.", type="error")
shinyjs::enable("btn__go")
return(1)
}
if(input$input__replacement == FALSE){
bad_sets <- c()
if(input$input__output_mode == "edf"){
if(input$input__num_synthetic_samples_pool < sum(unlist(lapply(manual_input_list, function(x) x$reps)))){
showNotification(paste0("Error: not enough samples will be generated to sample without replacement for dosage level(s): ", paste0(bad_sets, collapse=", "), ". Either increase the sample pool size or allow sampling with replacement."), type="error")
shinyjs::enable("btn__go")
return(1)
}
} else if(input$input__output_mode == "supp"){
bad_sets <- unlist(lapply(manual_input_list, function(x){
if(x$reps > input$input__num_synthetic_samples_pool){
return(x$dose)
}
}))
if(length(bad_sets) > 0){
showNotification(paste0("Error: not enough samples will be generated to sample without replacement for dosage level(s): ", paste0(bad_sets, collapse=", "), ". Either increase the sample pool size or allow sampling with replacement."), type="error")
shinyjs::enable("btn__go")
return(1)
}
}
}
}
if(input$input__output_mode == "noedf"){
proc_status <- generate_sample_pool(
mode="noedf",
input_mode=input$input__dose_input_type,
param__input_file=x[["Path"]],
param__input_file_name=x[["Filename"]],
param__output_file_path=paste0(set_uuid),
param__output_file_name=paste0(set_uuid, "__", x[["Filename"]]),
param__num_datafiles=1,
param__sample_pool=input$input__num_synthetic_samples,
param__num_treatment=input$input__num_treatment_groups,
param__num_repd0=input$input__num_synthetic_samples,
param__num_repnod0=0,
param__num_topdose=input$input__num_top_dose,
param__dose_spacing=input$input__dose_spacing,
param__manual_input=manual_input_list,
param__replacement_orig=input$input__replacement,
param__no_negative=input$input__noneg
)
} else if (input$input__output_mode == "edf"){
proc_status <- generate_sample_pool(
mode="edf",
input_mode=input$input__dose_input_type,
param__input_file=x[["Path"]],
param__input_file_name=x[["Filename"]],
param__output_file_path=paste0(set_uuid),
param__output_file_name=paste0(set_uuid, "__", x[["Filename"]]),
param__num_datafiles=input$input__num_edf,
param__sample_pool=input$input__num_synthetic_samples_pool,
param__num_treatment=input$input__num_treatment_groups,
param__num_repd0=input$input__num_rep_d0,
param__num_repnod0=input$input__num_rep_nod0,
param__num_topdose=input$input__num_top_dose,
param__dose_spacing=input$input__dose_spacing,
param__manual_input=manual_input_list,
param__replacement_orig=input$input__replacement,
param__no_negative=input$input__noneg
)
} else if (input$input__output_mode == "supp"){
proc_status <- generate_sample_pool(
mode="supp",
input_mode=input$input__dose_input_type,
param__input_file=x[["Path"]],
param__input_file_name=x[["Filename"]],
param__output_file_path=paste0(set_uuid),
param__output_file_name=paste0(set_uuid, "__", x[["Filename"]]),
param__num_datafiles=input$input__num_edf,
param__sample_pool=input$input__num_synthetic_samples_pool,
param__num_treatment=input$input__num_treatment_groups_supp,
param__num_repd0=input$input__num_rep_d0_supp,
param__num_repnod0=input$input__num_rep_nod0_supp,
param__num_topdose=input$input__num_top_dose_supp,
param__manual_input=manual_input_list,
param__replacement_orig=input$input__replacement,
param__no_negative=input$input__noneg
)
}
# error message handling
if(proc_status == 1){ # bad manual dosages
showNotification(paste0("Error (", x[["Filename"]], "): bad dosages supplied. Check that the dosage levels you have supplied match those in your input file and try again."), type="error")
shinyjs::enable("btn__go")
} else if(proc_status == 2){ # bad manual dosages
showNotification(paste0("Error (", x[["Filename"]], "): bad input file format. Ensure this input file is of the correct format."), type="error")
shinyjs::enable("btn__go")
} else if(proc_status == 3){ # no null samples provided
showNotification(paste0("Error (", x[["Filename"]], "): No null labels found in input file. You must supply null samples if synthesizing null data."), type="error")
shinyjs::enable("btn__go")
}
return(proc_status)
})
} else {
proc_status_list <- apply(reac__uploaded_files$dt, 1, function(x) c(x["Filename"], x["Path"]))
proc_status_list <- mclapply(proc_status_list, mc.silent=FALSE, mc.cores=N_CORES, function(x){
# parse out manual input ids
manual_input_list <- list()
if(input$input__dose_input_type == "manual"){
manual_input_list <- lapply(seq_len(length(names(reac__manual_input$el))), function(x){
list(
dose=input[[paste0("input__manual_dose__", names(reac__manual_input$el)[x])]],
reps=input[[paste0("input__manual_reps__", names(reac__manual_input$el)[x])]]
)
})
names(manual_input_list) <- names(reac__manual_input$el)
# Show error if no dosage levels specified
if(length(manual_input_list) < 1){
showNotification("Error: no dosage levels specified.", type="error")
shinyjs::enable("btn__go")
return(1)
}
if(input$input__replacement == FALSE){
bad_sets <- c()
if(input$input__output_mode == "edf"){
if(input$input__num_synthetic_samples_pool < sum(unlist(lapply(manual_input_list, function(x) x$reps)))){
showNotification(paste0("Error: not enough samples will be generated to sample without replacement for dosage level(s): ", paste0(bad_sets, collapse=", "), ". Either increase the sample pool size or allow sampling with replacement."), type="error")
shinyjs::enable("btn__go")
return(1)
}
} else if(input$input__output_mode == "supp"){
bad_sets <- unlist(lapply(manual_input_list, function(x){
if(x$reps > input$input__num_synthetic_samples_pool){
return(x$dose)
}
}))
if(length(bad_sets) > 0){
showNotification(paste0("Error: not enough samples will be generated to sample without replacement for dosage level(s): ", paste0(bad_sets, collapse=", "), ". Either increase the sample pool size or allow sampling with replacement."), type="error")
shinyjs::enable("btn__go")
return(1)
}
}
}
}
if(input$input__output_mode == "noedf"){
proc_status <- generate_sample_pool(
mode="noedf",
input_mode=input$input__dose_input_type,
param__input_file=x[["Path"]],
param__input_file_name=x[["Filename"]],
param__output_file_path=paste0(set_uuid),
param__output_file_name=paste0(set_uuid, "__", x[["Filename"]]),
param__num_datafiles=1,
param__sample_pool=input$input__num_synthetic_samples,
param__num_treatment=input$input__num_treatment_groups,
param__num_repd0=input$input__num_synthetic_samples,
param__num_repnod0=0,
param__num_topdose=input$input__num_top_dose,
param__dose_spacing=input$input__dose_spacing,
param__manual_input=manual_input_list,
param__replacement_orig=input$input__replacement,
param__no_negative=input$input__noneg
)
} else if (input$input__output_mode == "edf"){
proc_status <- generate_sample_pool(
mode="edf",
input_mode=input$input__dose_input_type,
param__input_file=x[["Path"]],
param__input_file_name=x[["Filename"]],
param__output_file_path=paste0(set_uuid),
param__output_file_name=paste0(set_uuid, "__", x[["Filename"]]),
param__num_datafiles=input$input__num_edf,
param__sample_pool=input$input__num_synthetic_samples_pool,
param__num_treatment=input$input__num_treatment_groups,
param__num_repd0=input$input__num_rep_d0,
param__num_repnod0=input$input__num_rep_nod0,
param__num_topdose=input$input__num_top_dose,
param__dose_spacing=input$input__dose_spacing,
param__manual_input=manual_input_list,
param__replacement_orig=input$input__replacement,
param__no_negative=input$input__noneg
)
} else if (input$input__output_mode == "supp"){
proc_status <- generate_sample_pool(
mode="supp",
input_mode=input$input__dose_input_type,
param__input_file=x[["Path"]],
param__input_file_name=x[["Filename"]],
param__output_file_path=paste0(set_uuid),
param__output_file_name=paste0(set_uuid, "__", x[["Filename"]]),
param__num_datafiles=input$input__num_edf,
param__sample_pool=input$input__num_synthetic_samples_pool,
param__num_treatment=input$input__num_treatment_groups_supp,
param__num_repd0=input$input__num_rep_d0_supp,
param__num_repnod0=input$input__num_rep_nod0_supp,
param__num_topdose=input$input__num_top_dose_supp,
param__manual_input=manual_input_list,
param__replacement_orig=input$input__replacement,
param__no_negative=input$input__noneg
)
}
# error message handling
if(proc_status == 1){ # bad manual dosages
showNotification(paste0("Error (", x[["Filename"]], "): bad dosages supplied. Check that the dosage levels you have supplied match those in your input file and try again."), type="error")
shinyjs::enable("btn__go")
} else if(proc_status == 2){ # bad manual dosages
showNotification(paste0("Error (", x[["Filename"]], "): bad input file format. Ensure this input file is of the correct format."), type="error")
shinyjs::enable("btn__go")
}
return(proc_status)
})
}
proc_status_list <- proc_status_list[proc_status_list == 0]
if(length(proc_status_list) > 0){
shinyjs::show("btn__download_zip")
# Show previews for generated files
outfiles <- Sys.glob(paste0("Simulated-Datasets/", dl_uuid$uuid, "/*"))
output$output__file_viz <- renderUI({
do.call(tabsetPanel,
lapply(paste0(outfiles), function(x){
tmp_panel <- tabPanel(
title=unlist(str_split(x, "/"))[3],
reactableOutput(outputId=paste0("tab__", x))
)
tryCatch({
tmp <- fread(x)
output[[paste0("tab__", x)]] <- renderReactable({
reactable(
tmp,
searchable=TRUE,
showPageSizeOptions=TRUE,
pageSizeOptions=c(10, 50, 100),
defaultPageSize=10
)
})
}, error=function(cond){
output[[paste0("tab__", x)]] <- renderReactable({data.frame()})
})
return(tmp_panel)
})
)
})
} else {
output$output__file_viz <- renderUI({"No files were generated."})
}
shinyjs::enable("btn__go")
})
output$btn__download_example <- downloadHandler(
filename=function() {
"Example_control.txt"
},
content=function(file) {
tmp <- fread(file="./examples/Example_control.txt", sep="\t", stringsAsFactors=FALSE)
fwrite(tmp, file, row.names=FALSE, sep="\t", quote=FALSE)
}
)
output$btn__download_example_mult <- downloadHandler(
filename=function() {
"Example_multiple_dose.txt"
},
content=function(file) {
tmp <- fread(file="./examples/Example_multiple_dose.txt", sep="\t", stringsAsFactors=FALSE)
fwrite(tmp, file, row.names=FALSE, sep="\t", quote=FALSE)
}
)
output$btn__download_zip <- downloadHandler(
filename=function() {
paste0(dl_uuid$uuid, ".zip")
},
content=function(file) {
# Zip files
curr_wd <- paste0(getwd(), "/")
files_to_zip <- paste0(curr_wd, "Simulated-Datasets/", dl_uuid$uuid, "/")
zip_path <- unlist(lapply(list.files(paste0(curr_wd, "Simulated-Datasets/", dl_uuid$uuid, "/")), function(x) paste0(curr_wd, "Simulated-Datasets/", dl_uuid$uuid, "/", x)))
zipr(zipfile=paste0(curr_wd, "Simulated-Datasets/", dl_uuid$uuid, ".zip"), files=zip_path)
file.copy(paste0(curr_wd, "Simulated-Datasets/", dl_uuid$uuid, ".zip"), file)
},
contentType = "application/zip"
)
}