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server.R
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server.R
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shinyServer(function(input, output, session) {
options(shiny.maxRequestSize=30*1024^2)
library("glmnet")
library("DT")
library("survival")
library("KMsurv")
library("survMisc")
source("lifeTables.R")
source("kaplanMeier.R")
source("coxRegression.R")
source("getDescriptiveResultsCoxRegression.R")
source("stepwise.R")
source("plotLT.R")
require("ggplot2")
source("ggsurv.R")
source("ggsurv2.R")
source("plotSchoenfeld.R")
library("magrittr")
library("dplyr")
library("survminer")
library("highcharter")
library("randomForestSRC")
library("pec")
library("knitr")
library("parallel")
source("cuttOffForSurvival.R")
source("get.event.info.R")
library("caret")
dataLoad <- reactive({ ## Data input.
if(input$dataInput==1){ ## Load example data.
# if(input$sampleData == 1){
#
# data <- read.table("www/data/bladderCancer.txt", header=TRUE, sep = "\t")
#
# data$time <- as.numeric(data$time)
# }
if(input$sampleData == 1){
isolate({
withProgress(message = 'Data upload in progress...', detail = 'This may take a while...', value = 1,{
data <- read.table("www/data/GSE2034.txt", header=TRUE, sep = "\t")
})
})
}
# else if(input$sampleData == 2){
#
# isolate({
#
# withProgress(message = 'Data upload in progress...', detail = 'This may take a while...', value = 1,{
#
#
# data <- read.table("www/data/GSE21257.txt", header=TRUE, sep = "\t")
# })
#
# })
# }
# else if(input$sampleData == 3){
#
# data <- read.table("www/data/GSE11121.txt", header=TRUE, sep = "\t")
#
# }
# else if(input$sampleData == 5){
#
# data <- read.table("www/data/heartTransplant.txt", header=TRUE, sep = "\t")
#
# }
#
# else if(input$sampleData == 6){
#
# data <- read.table("www/data/lupusNephritis.txt", header=TRUE, sep = "\t")
#
# }
#
# else if(input$sampleData == 7){
#
# data <- read.table("www/data/primaryBiliaryCirrhosis.txt", header=TRUE, sep = "\t")
#
# }
}
else if(input$dataInput==2){ ## Upload data.
inFile <- input$upload
mySep <- switch(input$fileSepDF, '1'=",",'2'="\t",'3'=";", '4'="")
if (is.null(input$upload)) {return(NULL)}
isolate({
withProgress(message = 'Data upload in progress...', detail = 'This may take a while...', value = 1,{
# if (file.info(inFile$datapath)$size <= 10485800){
data <- read.table(inFile$datapath, sep=mySep, header=TRUE, fill=TRUE, na.strings = c("", "NA","."))
# }
# else print("File is bigger than 10MB and will not be uploaded.")
})
})
}
ind = complete.cases(data)
data = data[ind,]
return(data)
#else {
# data[,dim(data)[2]] = as.factor(data[,dim(data)[2]])
# ind = complete.cases(data)
# return(data[ind,])
#}
})
dataN <- reactive({
if(input$preProcess && input$runProcess){
dataL = dataLoad()
if(!is.null(input$excludeVarsProcess)){
data = dataL[!(colnames(dataL) %in% c(input$survivalTimeProcess, input$statusVariableProcess, input$excludeVarsProcess))]
data2 = dataL[(colnames(dataL) %in% c(input$survivalTimeProcess, input$statusVariableProcess, input$excludeVarsProcess))]
}else{
data = dataL[!(colnames(dataL) %in% c(input$survivalTimeProcess, input$statusVariableProcess))]
data2 = dataL[(colnames(dataL) %in% c(input$survivalTimeProcess, input$statusVariableProcess))]
}
if (input$nearZero && input$runProcess){
nZ = nearZeroVar(data, saveMetrics = FALSE)
if(length(nZ) != 0){
nearZeroFeatures = nearZeroVar(data, saveMetrics = FALSE, names = TRUE)
data = data[-nZ]
}
}
if (input$center && input$runProcess){
if( TRUE %in% sapply(data, is.factor)){
stop("Dataset contains non-numeric variables. Pre-process can not be applied.")
}
else{
data = scale(data, center = TRUE, scale = FALSE)
}
}
if (input$scale && input$runProcess){
data = scale(data, center = FALSE, scale = TRUE)
}
if (input$transform && input$runProcess){
data = log(data+abs(min(data, na.rm=TRUE))+1)
}
dataNew = list(data = cbind.data.frame(data2, data), features = nearZeroFeatures)
}else{
dataNew = list(data = dataLoad(), features = NULL)
}
return(dataNew)
})
dataM <- reactive({
dataN()$data
})
nearZeroFeatures <- reactive({
if (input$nearZero && input$runProcess){
if(!is.null(dataN()$features)){
nearZeroFeatures = as.data.frame(dataN()$data)
# colnames(nearZeroFeatures) = "Near zero features"
return(nearZeroFeatures)
}else{
return(NULL)
}
}
})
output$nearZeroFeaturesResult <- DT::renderDataTable(server = FALSE, {
if (input$nearZero && input$runProcess){
datatable(nearZeroFeatures(), extensions = 'ColReorder', options = list(colReorder = TRUE))
}
})
output$dataUpload <- DT::renderDataTable(server = FALSE, {
datatable(dataM(), extensions = 'ColReorder', options = list(colReorder = TRUE))
})
################################ Observe Data Preporcess (start) ###############################
################################ Observe Data Preporcess (start) ###############################
observe({
if(input$preProcess){
updateSelectizeInput(session, "survivalTimeProcess", choices = colnames(dataM()), selected = colnames(dataM())[1])
}
})
observe({
if(input$preProcess){
updateSelectizeInput(session, "statusVariableProcess", choices = colnames(dataM()), selected = colnames(dataM())[2])
}
})
observe({
if(input$preProcess){
updateSelectizeInput(session, "excludeVarsProcess", choices = colnames(dataM()), selected = input$excludeVarsProcess)
}
})
# observe({
# updateSelectizeInput(session, "excludeVarsProcess", choices = colnames(dataM()[!(colnames(dataM()) %in% c(input$survivalTimeProcess, input$statusVariableProcess))]), selected = NULL)
# })
################################ Observe Life Table (start) ###############################
# observe({
# updateSelectInput(session, "statusVariable", choices = colnames(dataM()), selected = colnames(dataM())[4])
#})
observe({
updateSelectizeInput(session, "survivalTime", choices = colnames(dataM()), selected = colnames(dataM())[1])
})
observe({
if(input$factorVar){
updateSelectizeInput(session, "factor", choices = colnames(dataM()), selected = NULL)
}else{
updateSelectizeInput(session, "factor", choices = NULL, selected = NULL)
}
})
statusVarLT <- reactive({return(input$statusVariable)})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
updateSelectizeInput(session = session, inputId = "statusVariable",
choices = colnames(data_tmp), selected = colnames(data_tmp)[2])
} else {
updateSelectizeInput(session = session, inputId = "statusVariable",
choices = "", selected = "")
}
})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
idx <- which(colnames(data_tmp) %in% statusVarLT())
categories <- levels(as.factor(as.character(data_tmp[ ,idx])))
updateSelectizeInput(session = session, inputId = "status", choices = categories,
selected = categories[2])
} else {
updateSelectizeInput(session = session, inputId = "status", choices = "",
selected = "")
}
})
################################ Observe Life Table (end) ###############################
#########################################################################################
################################ Observe Kaplan-Meier (start) ###########################
observe({
updateSelectizeInput(session, "statusVariableKM", choices = colnames(dataM()), selected = colnames(dataM())[2])
})
observe({
updateSelectizeInput(session, "survivalTimeKM", choices = colnames(dataM()), selected = colnames(dataM())[1])
})
observe({
if(input$factorVarKM){
updateSelectizeInput(session, "factorKM", choices = colnames(dataM()), selected = colnames(dataM())[3])
}else{
updateSelectizeInput(session, "factoKMr", choices = NULL, selected = NULL)
}
})
statusVarKM <- reactive({return(input$statusVariableKM)})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
updateSelectizeInput(session = session, inputId = "statusVariableKM", choices = colnames(data_tmp), selected = colnames(data_tmp)[2])
} else {
updateSelectizeInput(session = session, inputId = "statusVariableKM", choices = "", selected = "")
}
})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
idx <- which(colnames(data_tmp) %in% statusVarKM())
categories <- levels(as.factor(as.character(data_tmp[ ,idx])))
updateSelectizeInput(session = session, inputId = "statusKM", choices = categories, selected = categories[2])
} else {
updateSelectizeInput(session = session, inputId = "statusKM", choices = "", selected = "")
}
})
#observe({
# if (input$selectPlotKM == 1){
# updateCheckboxInput(session, "kmPlotOptions", label = "Edit Plot", value = NULL)
# }
#})
################################ Observe Kaplan-Meier (end) ###########################
#########################################################################################
#########################################################################################
################################ Observe Cox Regression (start) ###########################
observe({
updateSelectizeInput(session, "survivalTimeCox", choices = colnames(dataM()), selected = colnames(dataM())[1])
})
#############################################################
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
updateSelectizeInput(session = session, inputId = "statusVariableCox", choices = colnames(data_tmp), selected = colnames(data_tmp[2]))
} else {
updateSelectizeInput(session = session, inputId = "statusVariableCox", choices = "", selected = "")
}
})
statusVarCox <- reactive({return(input$statusVariableCox)})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
idx <- which(colnames(data_tmp) %in% statusVarCox())
categories <- levels(as.factor(as.character(data_tmp[ ,idx])))
updateSelectizeInput(session = session, inputId = "statusCox", choices = categories, selected = categories[2])
} else {
updateSelectizeInput(session = session, inputId = "statusCox", choices = "", selected = "")
}
})
#############################################################
observe({
updateSelectizeInput(session, "categoricalInput", choices = colnames(dataM()), selected = colnames(dataM())[3])
})
observe({
updateSelectizeInput(session, "continuousInput", choices = colnames(dataM()), selected = colnames(dataM())[4])
})
observe({
if(input$twoWayInteractions || input$threeWayInteractions){
updateCheckboxInput(session, "customInteractions", value = FALSE)
}
if(input$customInteractions){
updateCheckboxInput(session, "twoWayInteractions", value = FALSE)
updateCheckboxInput(session, "threeWayInteractions", value = FALSE)
updateCheckboxInput(session, "customInteractions", value = TRUE)
}
})
observe({
if(input$customInteractions){
updateSelectizeInput(session, "selectCustomInteractions", choices = cInteractions(), selected = NULL)
}
})
observe({
if(input$addTimeDependentCovariates){
updateSelectizeInput(session, "selectTimeDependentVariables", choices = colnames(dataM()), selected = NULL)
}
})
strataVarNames <- reactive({
colnames(dataM())
})
observe({
if(input$addStrata){
updateSelectizeInput(session, "selectStrataVariable", choices = colnames(dataM()), selected = NULL)
}
})
################################ Observe Cox Regression (end) #########################
#######################################################################################
#########################################################################################
################################ Observe Regularized Cox Regression (start) ###########################
#########################################################################################
observe({
updateSelectizeInput(session, "survivalTimerCox", choices = colnames(dataM()), selected = colnames(dataM())[1])
})
observe({
data_tmp_rCox <- dataM()
if (!is.null(data_tmp_rCox)){
updateSelectizeInput(session = session, inputId = "statusVariablerCox", choices = colnames(data_tmp_rCox), selected = colnames(data_tmp_rCox)[2])
} else {
updateSelectizeInput(session = session, inputId = "statusVariablerCox", choices = "", selected = "")
}
})
statusVarrCox <- reactive({return(input$statusVariablerCox)})
observe({
data_tmp_rCox <- dataM()
if (!is.null(data_tmp_rCox)){
idx_rCox <- which(colnames(data_tmp_rCox) %in% statusVarrCox())
categories_rCox <- levels(as.factor(as.character(data_tmp_rCox[ ,idx_rCox])))
updateSelectizeInput(session = session, inputId = "statusrCox", choices = categories_rCox, selected = categories_rCox[2])
} else {
updateSelectizeInput(session = session, inputId = "statusrCox", choices = "", selected = "")
}
})
observe({
updateSelectizeInput(session, "categoricalVariablerCox", choices = colnames(dataM()), selected = NULL)
updateSelectizeInput(session, "numericalVariablerCox", choices = colnames(dataM()), selected = NULL)
})
################################ Observe Regularized Cox Regression (end) #########################
#######################################################################################
################################ Observe Random Survival Forest (start) ###########################
observe({
updateSelectizeInput(session, "survivalTimeRF", choices = colnames(dataM()), selected = colnames(dataM())[1])
})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
updateSelectizeInput(session = session, inputId = "statusVariableRF", choices = colnames(data_tmp), selected = colnames(data_tmp)[2])
} else {
updateSelectizeInput(session = session, inputId = "statusVariableRF", choices = "", selected = "")
}
})
statusVarRF <- reactive({return(input$statusVariableRF)})
observe({
data_tmp <- dataM()
if (!is.null(data_tmp)){
idx <- which(colnames(data_tmp) %in% statusVarRF())
categories <- levels(as.factor(as.character(data_tmp[ ,idx])))
updateSelectizeInput(session = session, inputId = "statusRF", choices = categories, selected = categories[2])
} else {
updateSelectizeInput(session = session, inputId = "statusRF", choices = "", selected = "")
}
})
observe({
updateSelectizeInput(session, "categoricalInputRF", choices = colnames(dataM()), selected = NULL)
})
observe({
updateSelectizeInput(session, "continuousInputRF", choices = colnames(dataM()), selected = NULL)
})
observe({
if(input$twoWayInteractionsRF || input$threeWayInteractionsRF){
updateCheckboxInput(session, "customInteractionsRF", value = FALSE)
}
if(input$customInteractionsRF){
updateCheckboxInput(session, "twoWayInteractionsRF", value = FALSE)
updateCheckboxInput(session, "threeWayInteractionsRF", value = FALSE)
updateCheckboxInput(session, "customInteractionsRF", value = TRUE)
}
})
observe({
if(input$customInteractionsRF){
updateSelectizeInput(session, "selectCustomInteractionsRF", choices = cInteractions(), selected = NULL)
}
})
observe({
if(input$addTimeDependentCovariatesRF){
updateSelectizeInput(session, "selectTimeDependentVariablesRF", choices = colnames(dataM()), selected = NULL)
}
})
strataVarNamesRF <- reactive({
colnames(dataM())
})
observe({
if(input$addStrataRF){
updateSelectizeInput(session, "selectStrataVariableRF", choices = colnames(dataM()), selected = NULL)
}
})
################################ Observe Random Survival Forest (end) #########################
#########################################################################################
################################ Observe Optimum cutoff(start) ###########################
#########################################################################################
observe({
updateSelectizeInput(session, "survivalTimeCutoff", choices = colnames(dataM()), selected = colnames(dataM())[1])
})
observe({
updateSelectizeInput(session, "selectMarkers", choices = colnames(dataM()), selected = colnames(dataM())[4])
})
observe({
data_tmp_Cutoff <- dataM()
if (!is.null(data_tmp_Cutoff)){
updateSelectizeInput(session = session, inputId = "statusVariableCutoff", choices = colnames(data_tmp_Cutoff), selected = colnames(data_tmp_Cutoff)[2])
} else {
updateSelectizeInput(session = session, inputId = "statusVariableCutoff", choices = "", selected = "")
}
})
statusCutoff <- reactive({return(input$statusVariableCutoff)})
observe({
data_tmp_Cutoff<- dataM()
if (!is.null(data_tmp_Cutoff)){
idx_Cutoff <- which(colnames(data_tmp_Cutoff) %in% statusCutoff())
categories_Cutoff <- levels(as.factor(as.character(data_tmp_Cutoff[ ,idx_Cutoff])))
updateSelectizeInput(session = session, inputId = "statusCutoff", choices = categories_Cutoff, selected = categories_Cutoff[2])
} else {
updateSelectizeInput(session = session, inputId = "statusCutoff", choices = "", selected = "")
}
})
################################ Observe Optimum cutoff (end) #########################
#######################################################################################
###################### Life Table (start) #############################################
output$newDataset <- renderText({
if (input$preProcess && input$nearZero){
'New Dataset'
}
})
output$descriptivesText <- renderText({
if (input$run && input$caseSummary){
'Table 1: Descriptives'
}
})
output$lifeTableText <- renderText({
if (input$run && input$lifeTable){
'Table 2: Life Table'
}
})
output$medianLifeTimeText <- renderText({
if (input$run && input$medianLifeTime){
'Table 3: Median Life Time'
}
})
output$hrText <- renderText({
if (input$run && input$hr){
'Table 4: Hazard Ratio'
}
})
output$compTestText <- renderText({
if (input$run && input$compTest && input$factorVar){
'Table 5: Comparison Tests'
}
})
result <- reactive({
if(input$run || input$createLTPlot){
dataSet = dataM()
if(input$factorVar){
fctr = input$factor
}else{fctr = NULL}
lt = lifeTables(survivalTime = input$survivalTime, statusVariable = input$statusVariable, status = input$status, factors= fctr, fromTime = input$from, toTime = input$to, by = input$by, lifeTable = input$lifeTable, descriptives = input$caseSummary, hr = input$hr, medianLifeTime = input$medianLifeTime, ci = input$ci,
varianceEstimation = input$varianceEstimation, compare = input$compTest, comparisonTest = input$comparisonTest, confidenceLevel = input$confidenceLevel,
referenceCategory = input$refCategory, typeOfTest = "asymptotic", p = input$pLT, q = input$qLT, data = dataSet)
lt
}
})
descriptivesReactive <- reactive({
if(input$run){
desc = result()$tableResult$caseSummary
if(!is.null(desc)){
if(input$factorVar){
descs = do.call(rbind.data.frame, desc)
}else{
descs = desc
}
}else{descs = NULL}
descs
}else{descs = NULL}
})
output$descriptives <- DT::renderDataTable(server = FALSE, {
datatable(descriptivesReactive(), extensions = c('Buttons','KeyTable', 'Responsive'), options = list(
dom = 'Bfrtip',
buttons = list('copy', 'print', list( extend = 'collection', buttons = c('csv', 'excel', 'pdf'), text = 'Download' )), keys = TRUE
))
})
lifetableReactive <- reactive({
if(input$run){
ltResult = result()$testResult$lifeTable
if(!is.null(ltResult)){
if(input$factorVar){
ltResults = do.call(rbind.data.frame, ltResult)
}else{
ltResults = ltResult
}
}else{ltResults = NULL}
ltResults
}else{ltResults = NULL}
})
output$lifetableResult <- DT::renderDataTable(server = FALSE, {
datatable(lifetableReactive(), extensions = c('Buttons','KeyTable', 'Responsive'), options = list(
dom = 'Bfrtip',
buttons = list('copy', 'print', list( extend = 'collection', buttons = c('csv', 'excel', 'pdf'), text = 'Download' )), keys = TRUE
))
})
medianLifeTimeReactive <- reactive({
if(input$run){
mlt = result()$tableResult$medianLifeTime
if(!is.null(mlt)){
if(input$factorVar){
mltResults = do.call(rbind.data.frame, mlt)
}else{
mltResults = mlt
}
}else{mltResults = NULL}
mltResults
}else{mltResults = NULL}
})
output$medianLifeTimeResult <- DT::renderDataTable(server = FALSE, {
datatable(medianLifeTimeReactive(), extensions = c('Buttons','KeyTable', 'Responsive'), options = list(
dom = 'Bfrtip',
buttons = list('copy', 'print', list( extend = 'collection', buttons = c('csv', 'excel', 'pdf'), text = 'Download' )), keys = TRUE
))
})
hazardRatioReactive <- reactive({
if(input$run){
hrResult = result()$testResult$hazardRatio
if(!is.null(hrResult)){
if(input$factorVar){
hrResults = do.call(rbind.data.frame, hrResult)
}else{
hrResults = hrResult
}
}else{hrResults = NULL}
hrResults
}else{hrResults = NULL}
})
output$hazardRatioResult <- DT::renderDataTable(server = FALSE, {
datatable(hazardRatioReactive(), extensions = c('Buttons','KeyTable', 'Responsive'), options = list(
dom = 'Bfrtip',
buttons = list('copy', 'print', list( extend = 'collection', buttons = c('csv', 'excel', 'pdf'), text = 'Download' )), keys = TRUE
))
})
comparisonTestReactive <- reactive({
if(input$factorVar && input$compTest && input$run){
compTestResult = result()$testResult$testResults
}else{
compTestResult = NULL
}
})
output$comparisonTestResults <- DT::renderDataTable(server = FALSE, {
datatable(comparisonTestReactive(), extensions = c('Buttons','KeyTable', 'Responsive'), options = list(
dom = 'Bfrtip',
buttons = list('copy', 'print', list( extend = 'collection', buttons = c('csv', 'excel', 'pdf'), text = 'Download' )), keys = TRUE
))
})
###################### Life Table (end) #######################################################
###############################################################################################
###################### Kaplan-Meier (start) ###################################################
output$descriptivesTextKM <- renderText({
if (input$runKM && input$caseSummaryKM){
'Table 1: Descriptives'
}
})
output$survivalTableTextKM <- renderText({
if (input$runKM && input$survivalTable){
'Table 2: Survival Table'
}
})
output$meanMedianSurvivalTimesText <- renderText({
if (input$runKM && input$meanMedianSurvivalTimes){
'Table 3: Mean and Median Life Time'
}
})
#output$quartilesOfSurvivalTimesText <- renderText({
# if (input$runKM && input$quartilesOfSurvivalTimes){
# 'Table 4: Quartiles of Survival Times'
# }
#})
output$hrTextKM <- renderText({
if (input$runKM && input$hrKM){
'Table 4: Hazard Ratio'
}
})
output$compTestTextKM <- renderText({
if (input$runKM && input$compTestKM && input$factorVarKM){
'Table 5: Comparison Tests'
}
})
resultKM <- reactive({
if(input$runKM){
isolate({
withProgress(message = 'Kaplan-Meier in progress...', detail = 'This may take a while...', value = 1,{
dataSet = dataM()
if(input$factorVarKM){
fctr = input$factorKM
}else{fctr = NULL}
km = kaplanMeier (survivalTime = input$survivalTimeKM, statusVariable = input$statusVariableKM, status = input$statusKM, factors = fctr, survivalTable = TRUE, caseSummary = input$caseSummaryKM, hr=input$hrKM,
meanMedianSurvivalTimes = input$meanMedianSurvivalTimes, quartilesOfSurvivalTimes = FALSE, ci = input$ciKM,
varianceEstimation = input$varianceEstimationKM, comparisonTest = input$comparisonTestKM, confidenceLevel = input$confidenceLevelKM,
referenceCategory = input$refCategoryKM, typeOfTest = "asymptotic", kmCurve = TRUE, p = input$pKM, q = input$qKM, data = dataSet)
km
})
})
}
})
descriptivesReactiveKM <- reactive({
if(input$runKM && input$caseSummaryKM){
desc = resultKM()$tableResult$caseSummary
if(!is.null(desc)){
if(input$factorVarKM){
descs = do.call(rbind.data.frame, desc)
}else{
descs = desc
}
}else{descs = NULL}
descs
}else{descs = NULL}
})
output$descriptivesKM <- DT::renderDataTable(server = FALSE, {