R/analysis_survival.R

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

#' @rdname appUI
#'
#' @importFrom shinyBS bsTooltip
#' @importFrom shiny NS tagList uiOutput sidebarPanel radioButtons helpText hr
#' selectizeInput checkboxInput sliderInput actionButton mainPanel textAreaInput
#' conditionalPanel
#' @importFrom shinyjs hidden
survivalUI <- function(id) {
    ns <- NS(id)

    kaplanMeierOptions <- tagList(
        checkboxInput(ns("markTimes"), "Show censored observations",
                      value = TRUE),
        checkboxInput(ns("ranges"), "Show interval ranges", value = FALSE))

    modelChoices <- c(
        "No groups"="none",
        "Clinical groups (simple)"="groups",
        "Clinical groups (including their interactions)"="formula",
        "Gene expression cutoff from the selected gene"="geCutoff",
        "Inclusion levels cutoff from the selected splicing event"="psiCutoff")

    survivalTimeOptions <- tagList(
        radioButtons(ns("censoring"), "Data censoring", selected="right",
                     inline=TRUE, choices=c(Left="left", Right="right",
                                            Interval="interval",
                                            "Interval 2" = "interval2")),
        selectizeInput(ns("timeStart"), "Follow up time",
                       choices=c("No clinical data loaded"="")),
        # If chosen censoring contains the word 'interval', ask end time
        conditionalPanel(
            paste0("input[id='", ns("censoring"),
                   "'].indexOf('interval') > -1"),
            selectizeInput(ns("timeStop"), "Ending time",
                           choices=c("No clinical data loaded"=""))),
        helpText("For subjects with no event reported, time to last follow up",
                 "is used instead."),
        selectizeInput(ns("event"), "Event of interest",
                       choices=c("No clinical data loaded"="")),
        radioButtons(
            ns("scale"), "Display time in", inline=TRUE,
            c(Days="days", Weeks="weeks", Months="months", Years="years")))

    survivalGroups <- tagList(
        radioButtons(ns("modelTerms"), selected="groups",
                     div("Select groups for survival analysis",
                         icon("question-circle")), choices=modelChoices),
        bsTooltip(
            ns("modelTerms"), placement="right",
            options = list(container = "body"),
            paste(
                "Perform survival analysis using:", tags$br(), "\u2022",
                "User-created", tags$b("clinical groups"), tags$br(),
                "\u2022 A formula that can test clinical attributes with",
                tags$b("interactions"), tags$br(),
                "\u2022", tags$b("Gene expression cutoff"), "based on the",
                "selected gene", tags$br(),
                "\u2022", tags$b("Inclusion levels cutoff"), "from the",
                "selected alternative splicing event")),
        conditionalPanel(
            sprintf("input[id='%s'] == '%s'", ns("modelTerms"), "groups"),
            selectGroupsUI(
                ns("dataGroups"), type="Samples",
                label=NULL, returnAllDataValue=FALSE,
                returnAllDataLabel="Display data outside selected groups")),
        conditionalPanel(
            sprintf("input[id='%s'] == '%s'", ns("modelTerms"), "formula"),
            textAreaInput(
                ns("formula"), "Formula with clinical attributes",
                placeholder="Type to show attribute suggestions"),
            uiOutput(ns("formulaSuggestions")),
            helpText(
                "To analyse a series of attributes, separate each",
                "attribute with a", tags$kbd("+"), ". To analyse",
                "interactions, use", tags$kbd(":"), " (interactions are",
                "only usable with Cox models). For example, ",
                tags$kbd("tumor_stage : gender + race"), br(), br(),
                "Interesting attributes include", tags$b("tumor_stage"),
                "to get tumour stages.")),
        conditionalPanel(
            sprintf("input[id='%s'].includes('%s')", ns("modelTerms"),
                    "Cutoff"),
            selectGroupsUI(ns("sampleFiltering"), type="Samples",
                           label=div(id=ns("helpFiltering"), "Sample filtering",
                                     icon("question-circle"))),
            bsTooltip(ns("helpFiltering"), options=list(container="body"),
                      placement="right", subjectMultiMatchWarning())),
        conditionalPanel(
            sprintf("input[id='%s'] == '%s'", ns("modelTerms"), "geCutoff"),
            hidden(selectizeInput(
                ns("geneExpr"), "Gene expression", width="100%",
                choices=c("No gene expression available"=""))),
            hidden(div(id=ns("loadingGenes"), class="progress",
                       div(class="progress-bar progress-bar-striped active",
                           role="progressbar", style="width:100%",
                           "Loading available genes"))),
            hidden(selectizeGeneInput(ns("gene"))),
            hidden(sliderInput(ns("geCutoff"), value=0.5, min=0, max=1,
                               step=0.01, round=-2, "Gene expression cutoff")),
            hidden(uiOutput(ns("geInfo"))),
            uiOutput(ns("gePvaluePlot"))),
        conditionalPanel(
            sprintf("input[id='%s'] == '%s'", ns("modelTerms"), "psiCutoff"),
            hidden(sliderInput(ns("psiCutoff"), value=0.5, min=0, max=1,
                               step=0.01, "Splicing quantification cutoff")),
            uiOutput(ns("pvaluePlot"))))

    survival <- div(
        id=ns("survivalOptions"),
        bsCollapse(open=c("survivalTimeOptions", "survivalGroups", "KMoptions"),
                   multiple=TRUE,
                   bsCollapsePanel(
                       tagList(icon("calendar-times"),
                               "Selection of time features"),
                       value="survivalTimeOptions", style="info",
                       survivalTimeOptions),
                   bsCollapsePanel(
                       tagList(icon("users"), "Groups for survival analysis"),
                       value="survivalGroups", style="info", survivalGroups),
                   bsCollapsePanel(
                       tagList(icon("check-square"),
                               "Kaplan-Meier plot options"),
                       value="KMoptions", style="info", kaplanMeierOptions)),
        actionButton(ns("coxModel"), "Fit Cox PH model"),
        actionButton(ns("survivalCurves"), class="btn-primary",
                     "Plot survival curves"))

    tagList(
        uiOutput(ns("modal")),
        sidebarPanel(
            errorDialog("Clinical data not loaded.",
                        id=ns("survivalDialog"),
                        buttonId=ns("loadClinical"),
                        buttonLabel="Load clinical data"),
            hidden(survival)
        ),
        mainPanel(
            highchartOutput(ns("survival")),
            uiOutput(ns("coxphUI"))
        )
    )
}

#' Prepare survival terms in case of valid input
#'
#' @inheritParams appServer
#' @param coxph Boolean: prepare data for Cox models?
#'
#' @inherit psichomics return
#' @keywords internal
checkSurvivalInput <- function (session, input, coxph=FALSE) {
    ns <- session$ns

    isolate({
        subjects      <- getSubjectId()
        match         <- getClinicalMatchFrom("Inclusion levels")
        splicingEvent <- getEvent()
        # Get user input
        timeStart  <- input$timeStart
        timeStop   <- input$timeStop
        event      <- input$event
        censoring  <- input$censoring
        outGroup   <- input$dataGroupsShowAllData
        modelTerms <- input$modelTerms
        formulaStr <- input$formula
        scale      <- input$scale
        # Get chosen groups
        chosen  <- getSelectedGroups(input, "dataGroups", "Patients")
        samples <- getSelectedGroups(input, "sampleFiltering", "Samples")
        # Get clinical data for the required attributes
        followup <- "days_to_last_followup"
        clinical <- getClinicalDataForSurvival(timeStart, timeStop, event,
                                               followup, formulaStr=formulaStr)
    })

    if (outGroup)
        outGroupName <- "(Outer data)"
    else
        outGroupName <- NA

    if ( is.null(subjects) ) {
        missingDataModal(session, "Clinical data", ns("missingClinical"))
        return(NULL)
    } else if (modelTerms == "none") {
        groups <- groupPerElem(NULL, subjects, outGroupName)
        formulaStr <- NULL
    } else if (modelTerms == "groups") {
        # Assign one group for each clinical subject
        groups <- groupPerElem(chosen, subjects, outGroupName)
        formulaStr <- NULL
    } else if (modelTerms == "geCutoff") {
        isolate({
            geneExpr <- getGeneExpression(input$geneExpr)
            gene     <- input$gene
            geCutoff <- input$geCutoff
        })

        if (is.null(geneExpr)) {
            missingDataModal(session, "Gene Expression",
                             ns("missingGeneExpression"))
            return(NULL)
        } else if (is.null(gene) || gene == "") {
            errorModal(session, "No gene selected", "Please select a gene.",
                       caller="Survival analysis")
            return(NULL)
        }

        # Assign values to subjects based on their samples
        eventGE <- assignValuePerSubject(geneExpr[gene, ], match,
                                         patients=subjects,
                                         samples=unlist(samples))

        # Assign a value based on the inclusion levels cutoff
        groups <- labelBasedOnCutoff(eventGE, geCutoff, "Gene expression")
        formulaStr <- NULL
    } else if (modelTerms == "psiCutoff") {
        isolate({
            psi       <- getInclusionLevels()
            psiCutoff <- input$psiCutoff
        })

        if (is.null(psi)) {
            missingDataModal(session, "Inclusion levels",
                             ns("missingInclusionLevels"))
            return(NULL)
        } else if (is.null(splicingEvent) || splicingEvent == "") {
            errorModal(session, "No event selected",
                       "Select an alternative splicing event.",
                       caller="Survival analysis")
            return(NULL)
        }

        # Assign values to subjects based on their samples
        eventPSI <- assignValuePerSubject(psi[splicingEvent, ], match,
                                          patients=subjects,
                                          samples=unlist(samples))

        # Assign a value based on the inclusion levels cutoff
        groups <- labelBasedOnCutoff(eventPSI, psiCutoff, "Inclusion levels")
        formulaStr <- NULL
    } else if (modelTerms == "formula") {
        if (input$formula == "" || is.null(input$formula)) {
            errorModal(session, "Empty formula",
                       "Please fill the formula field.",
                       caller="Survival analysis")
            return(NULL)
        } else {
            groups <- NULL
        }
    }

    interval <- grepl("interval", censoring)
    if (event == "") {
        errorModal(session, "No event selected",
                   "Please select the event of interest.",
                   caller="Survival analysis")
    } else if (timeStart == "") {
        if (!interval) {
            errorModal(session, "No follow up time selected",
                       "Please select follow up time.",
                       caller="Survival analysis")
        } else {
            errorModal(session, "No starting time selected",
                       "Please select starting time.",
                       caller="Survival analysis")
        }
    } else if (timeStop == "" && interval) {
        errorModal(session, "No ending time selected",
                   "Please select ending time to use interval censoring.",
                   caller="Survival analysis")
    } else {
        survTerms <- processSurvival(session, clinical, censoring, event,
                                     timeStart, timeStop, groups, formulaStr,
                                     scale=scale, coxph=coxph)
        attr(survTerms, "Colour") <- attr(groups, "Colour")
        return(survTerms)
    }
}

#' Logic set to perform survival analysis based on gene expression cutoffs
#'
#' @inheritParams survivalServer
#'
#' @importFrom shinyjs show hide
#'
#' @inherit psichomics return
#' @keywords internal
geneExprSurvSet <- function(session, input, output) {
    # Update available gene expression data choices
    observe({
        geneExpr <- getGeneExpression()
        if (!is.null(geneExpr)) {
            updateSelectizeInput(session, "geneExpr",
                                 choices=rev(names(geneExpr)))
            show("geneExpr")
        } else {
            hide("geneExpr")
        }
    })

    # Update available gene choices depending on gene expression data loaded
    # Reactive avoids updating if the input remains the same
    updateGeneChoices <- reactive({
        geneExpr <- getGeneExpression(input$geneExpr)
        genes <- rownames(geneExpr)
        updateSelectizeInput(session, "gene", choices=genes, server=TRUE)
    })

    # Update available gene choices depending on gene expression data loaded
    observe({
        geneExpr <- getGeneExpression(input$geneExpr)
        if (!is.null(geneExpr) && input$modelTerms == "geCutoff") {
            show("loadingGenes")
            hide("gene")

            updateGeneChoices()

            hide("loadingGenes")
            show("gene")
            show("geCutoff")
            show("geInfo")
        } else {
            hide("loadingGenes")
            hide("gene")
            hide("geCutoff")
            hide("geInfo")
        }
    })

    # Update gene expression cutoff values based on selected gene
    # Reactive avoids updating if the input remains the same
    updateGEcutoffSlider <- reactive({
        geneExpr <- getGeneExpression(input$geneExpr)
        ge <- as.numeric(geneExpr[input$gene, ])
        updateSliderInput(session, "geCutoff", min=roundMinDown(ge, 2),
                          max=roundMaxUp(ge, 2), value=round(mean(ge), 2))
    })

    # Update gene expression cutoff values based on selected gene
    observeEvent(input$gene, {
        geneExpr <- getGeneExpression(input$geneExpr)
        if (!is.null(geneExpr) && input$gene != "" &&
            input$modelTerms == "geCutoff") {
            updateGEcutoffSlider()
            enable("geCutoff")
        } else {
            disable("geCutoff")
        }
    })

    # Update gene information based on selected gene
    observe({
        geneExpr <- getGeneExpression(input$geneExpr)
        gene     <- input$gene
        terms    <- input$modelTerms

        subjects <- getSubjectId()
        match    <- getClinicalMatchFrom("Inclusion levels")
        # Get user input
        timeStart <- input$timeStart
        timeStop  <- input$timeStop
        event     <- input$event
        censoring <- input$censoring
        samples   <- getSelectedGroups(input, "sampleFiltering", "Samples")
        # Get clinical data for the required attributes
        followup <- "days_to_last_followup"
        clinical <- getClinicalDataForSurvival(timeStart, timeStop, event,
                                               followup)

        ui <- NULL
        if (!is.null(geneExpr) && !is.null(gene) && !identical(gene, "") &&
            terms == "geCutoff" && !is.null(clinical)) {

            # Assign gene expression values to subjects based on their samples
            eventGE <- assignValuePerSubject(geneExpr[gene, ], match,
                                             patients=subjects,
                                             samples=unlist(samples))

            # Mean gene expression cutoff
            meanGEcutoff <- round(mean(eventGE, na.rm=TRUE), 2)
            label        <- labelBasedOnCutoff(eventGE, meanGEcutoff,
                                               label="Gene expression")
            survTerms    <- processSurvTerms(clinical, censoring=censoring,
                                             event=event, timeStart=timeStart,
                                             timeStop=timeStop,
                                             followup=followup, group=label)
            meanGEpvalue <- testSurvival(survTerms)

            updateSliderInput(session, "geCutoff", value=meanGEcutoff)

            # Optimal gene expression cutoff
            opt       <- optimalSurvivalCutoff(clinical, eventGE,
                                               censoring=censoring,
                                               event=event, timeStart=timeStart,
                                               timeStop=timeStop,
                                               session=session)

            optimal   <- round(opt$par, 2)
            label     <- labelBasedOnCutoff(eventGE, optimal,
                                            label="Gene expression")
            survTerms <- processSurvTerms(clinical, censoring=censoring,
                                          event=event, timeStart=timeStart,
                                          timeStop=timeStop, followup=followup,
                                          group=label)
            optPvalue <- testSurvival(survTerms)

            df <- data.frame(c("Mean expression", "Optimal cutoff"),
                             c(meanGEcutoff, optimal),
                             paste("p-value:", c(meanGEpvalue, optPvalue)))
            ui <- table2html(df, rownames=FALSE, colnames=FALSE, class="table")

            addLinkToUpdateSliderValue <- function(val) {
                val  <- format(val, nsmall=2)
                link <- linkToRunJS(val, sprintf("setGEcutoffSlider(%s)", val))
                gsub(val, link, ui, fixed=TRUE)
            }

            ui <- addLinkToUpdateSliderValue(meanGEcutoff)
            ui <- addLinkToUpdateSliderValue(optimal)
        }

        output$geInfo <- renderUI(tags$html(ui))
        # output$geInfo <- renderUI(tagList(helpText(meanGEtext),
        #                                   helpText(optGEtext)))
    })

    observe({
        subjects <- getSubjectId()
        geneExpr <- getGeneExpression(input$geneExpr)
        gene     <- input$gene

        if (is.null(subjects)) {
            hide("geOptions")
            info <- helpText(icon("exclamation-circle"),
                             "Please load clinical data.")
        } else if (is.null(geneExpr)) {
            hide("geOptions")
            info <- helpText(icon("exclamation-circle"),
                             "Please load gene expression data.")
        } else {
            info <- NULL
        }

        output$gePvaluePlot <- renderUI(info)
    })
}

#' Plot p-values of survival difference between groups based on multiple cutoffs
#'
#' @inheritParams processSurvTerms
#' @inheritParams testSurvivalCutoff
#' @param significance Numeric: significance threshold
#' @param cutoffs Numeric: cutoffs to test
#'
#' @family functions to analyse survival
#' @return p-value plot
#' @export
#'
#' @examples
#' clinical <- read.table(text = "2549   NA ii  female
#'                                 840   NA i   female
#'                                  NA 1204 iv    male
#'                                  NA  383 iv  female
#'                                1293   NA iii   male")
#' names(clinical) <- c("patient.days_to_last_followup",
#'                      "patient.days_to_death",
#'                      "patient.stage_event.pathologic_stage",
#'                      "patient.gender")
#' clinical <- do.call(rbind, rep(list(clinical), 5))
#' rownames(clinical) <- paste("Subject", seq(nrow(clinical)))
#'
#' # Calculate PSI for skipped exon (SE) and mutually exclusive (MXE) events
#' annot <- readFile("ex_splicing_annotation.RDS")
#' junctionQuant <- readFile("ex_junctionQuant.RDS")
#'
#' psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))
#'
#' # Match between subjects and samples
#' match <- c("Cancer 1"="Subject 3",
#'            "Cancer 2"="Subject 17",
#'            "Cancer 3"="Subject 21")
#'
#' eventData <- assignValuePerSubject(psi[3, ], match)
#'
#' event      <- "days_to_death"
#' timeStart  <- "days_to_death"
#' plotSurvivalPvaluesByCutoff(clinical, eventData, censoring="right",
#'                             event=event, timeStart=timeStart)
plotSurvivalPvaluesByCutoff <- function(
    clinical, data, censoring, event, timeStart, timeStop=NULL,
    followup="days_to_last_followup", significance=0.05,
    cutoffs=seq(0, 0.99, 0.01)) {

    survTime <- getAttributesTime(clinical, event, timeStart, timeStop)

    pvalues <- lapply(
        cutoffs, testSurvivalCutoff, data=data,
        clinical=clinical, censoring=censoring, timeStart=timeStart,
        timeStop=timeStop, event=event, survTime=survTime, survivalInfo=TRUE)

    subjects     <- lapply(pvalues, function(n) attr(n, "info")$n)
    noSeparation <- vapply(subjects, length, numeric(1)) == 1
    subjects[noSeparation] <- NA
    subjects1 <- vapply(subjects, "[[", 1, FUN.VALUE = numeric(1))
    subjects2 <- NA
    subjects2[!noSeparation] <- vapply(subjects[!noSeparation],
                                       "[[", 2, FUN.VALUE = numeric(1))

    minusLog10pvalues <- -log10(unlist(pvalues))
    minusLog10signif  <- -log10(significance)

    data <- data.frame(x=cutoffs, y=minusLog10pvalues,
                       patients1=subjects1, patients2=subjects2)
    data <- list_parse(data)

    firstSeriesColour <- JS("Highcharts.getOptions().colors[0]")

    # Put the label of p-value plot to the right when there are many
    # significant points to the left
    signif <- minusLog10pvalues >= minusLog10signif
    labelAlign <- "left"
    if (sum(signif[seq(50)]) > sum(signif[51:100])) labelAlign <- "right"

    pvaluePlot <- highchart(height="100px") %>%
        hc_add_series(data=data,
                      zones=list(list(value=minusLog10signif,
                                      color="lightgray"))) %>%
        hc_chart(zoomType="x") %>%
        hc_xAxis(tickInterval=0.1, showLastLabel=TRUE, endOnTick=TRUE,
                 min=0, max=1, minorGridLineWidth=0,
                 gridLineWidth=0) %>%
        hc_yAxis(crosshair=list(color="gray", width=1,
                                dashStyle="shortdash"),
                 labels=list(enabled=FALSE), gridLineWidth=0,
                 plotLines=list(list(
                     value=significance, color=firstSeriesColour,
                     dashStyle="shortdash", width=1,
                     label=list(
                         align=labelAlign, text=paste("p <", significance),
                         style=list(color=firstSeriesColour))))) %>%
        hc_legend(NULL) %>%
        hc_tooltip(formatter=JS(
            "function() { return getPvaluePlotTooltip(this); }")) %>%
        hc_plotOptions(series=list(
            cursor="pointer",
            point=list(events=list(click=JS(
                "function () { setPSIcutoffSlider(this.x) }"))),
            marker=list(radius=2)))
    attr(pvaluePlot, "pvalues") <- pvalues
    return(pvaluePlot)
}

#' @rdname appServer
#'
#' @importFrom R.utils capitalize
#' @importFrom shiny renderUI observe updateSelectizeInput observeEvent isolate
#' br tagList hr div icon updateSliderInput uiOutput renderUI
#' @importFrom stats pchisq optim
#' @importFrom survival survdiff
#' @importFrom highcharter hchart hc_chart hc_yAxis hc_xAxis hc_tooltip
#' hc_subtitle hc_tooltip renderHighchart hc_plotOptions
#' @importFrom DT dataTableOutput renderDataTable
#' @importFrom utils write.table
#' @importFrom shinyjs show hide
survivalServer <- function(input, output, session) {
    ns <- session$ns

    selectGroupsServer(session, "dataGroups", "Samples")
    selectGroupsServer(session, "sampleFiltering", "Samples",
                       # Prefer TCGA tumour samples
                       preference="Primary solid Tumor")

    observe({
        if ( is.null(getSubjectAttributes()) ) {
            show("survivalDialog")
            hide("survivalOptions")
        } else {
            hide("survivalDialog")
            show("survivalOptions")
        }
    })
    observeEvent(input$loadClinical, missingDataGuide("Clinical data"))

    # Update available clinical data attributes to use in a formula
    output$formulaSuggestions <- renderUI({
        textSuggestions(ns("formula"), getSubjectAttributes())
    })

    # Update selectize input label depending on the chosen censoring type
    observe({
        label <- "Follow up time"
        if (grepl("interval", input$censoring, fixed=TRUE))
            label <- "Starting time"
        updateSelectizeInput(session, "timeStart", label=label)
    })

    # Update available clinical attributes when the clinical data changes
    observe( updateClinicalParams(session, getSubjectAttributes()) )

    observeEvent(input$missingClinical, missingDataGuide("Clinical data"))
    observeEvent(input$missingInclusionLevels,
                 missingDataGuide("Inclusion levels"))
    observeEvent(input$missingGeneExpression,
                 missingDataGuide("Gene expression"))

    # Plot survival curves
    observeEvent(input$survivalCurves, {
        isolate({
            splicingEvent <- getEvent()
            # Get user input
            modelTerms <- input$modelTerms
            intRanges  <- input$ranges
            markTimes  <- input$markTimes
            psiCutoff  <- input$psiCutoff
            scale      <- input$scale
        })

        survTerms <- checkSurvivalInput(session, input)
        if (is.null(survTerms)) return(NULL)

        surv <- tryCatch(survfit(survTerms), error=return)
        if ("simpleError" %in% class(surv)) {
            errorModal(session, "Formula error",
                       "The following error was raised:", br(),
                       tags$code(surv$message),
                       caller="Survival analysis")
            return(NULL)
        }

        pvalue <- testSurvival(survTerms)

        if (modelTerms == "psiCutoff") {
            plotTitle <- parseSplicingEvent(splicingEvent, char=TRUE,
                                            pretty=TRUE)
            sub <- paste0("PSI cutoff: ", psiCutoff,
                          "; Log-rank p-value: ", pvalue)
        } else {
            plotTitle <- "Survival analysis"
            sub <- NULL
        }

        # Plot survival curves
        attr(surv, "Colour") <- attr(survTerms, "Colour")
        hc <- plotSurvivalCurves(surv, markTimes, intRanges, pvalue, plotTitle,
                                 scale) %>% export_highcharts()
        if (!is.null(sub)) hc <- hc_subtitle(hc, text=sub)
        output$survival <- renderHighchart(hc)
    })

    # Fit Cox Proportional Hazards model
    observeEvent(input$coxModel, {
        survTerms <- checkSurvivalInput(session, input, coxph=TRUE)

        if (!is.null(survTerms)) {
            # Properly set group names
            names(survTerms$coefficients) <-
                gsub("&gt;", ">", names(survTerms$coefficients), fixed=TRUE)
            names(survTerms$coefficients) <-
                gsub("&lt;", "<", names(survTerms$coefficients), fixed=TRUE)

            summary <- summary(survTerms)
            print(summary)

            if (is.null(survTerms$coef)) {
                warningModal(session, "Null Cox model",
                             "Obtained a null Cox model.",
                             caller="Survival analysis")
                survTerms <- NULL
            } else {
                # General statistical tests
                tests <- rbind("Wald test"=summary$waldtest,
                               "Log test"=summary$logtest,
                               "Score (logrank) test"=summary$sctest)
                colnames(tests) <- c("Value", "Degrees of freedom", "p-value")

                # Groups statistics
                cox <- cbind(summary$coefficients,
                             summary$conf.int[ , 2:4, drop=FALSE])

                # Properly set colnames and order them
                colnames(cox) <- c("Coefficient", "Hazard ratio",
                                   "Standard error", "Wald test", "p-value",
                                   "1 / Hazard ratio", "Lower 95%", "Upper 95%")
                cox <- cox[ , c(1, 3:2, 7:8, 6, 4:5), drop=FALSE]
            }
        }

        output$coxphUI <- renderUI({
            if (is.null(survTerms)) return(NULL)

            len <- length(summary$na.action)
            tagList(
                hr(),
                downloadButton(ns("download"), "Save Cox model information",
                               class="pull-right btn-info"),
                h3("Cox", tags$abbr("PH", title="Proportional Hazards"),
                   "model", tags$small(
                       summary$n, " subjects with ", summary$nevent, " events",
                       if (len > 0)
                           paste0(" (", len, " missing values removed)"))),
                tags$b("Concordance: "), roundDigits(summary$concordance[[1]]),
                tags$b("(standard error: "),
                roundDigits(summary$concordance[[2]]), tags$b(")"),
                br(), tags$b("R\u00B2: "), roundDigits(summary$rsq[[1]]),
                tags$b("(max possible: "), roundDigits(summary$rsq[[2]]),
                tags$b(")"),
                dataTableOutput(ns("coxTests")), hr(),
                dataTableOutput(ns("coxGroups"))
            )
        })

        output$download <- downloadHandler(
            filename=paste(getCategory(), "Cox PH model", Sys.Date(), ".txt"),
            content=function(file) {
                len <- length(summary$na.action)
                info <- paste0(
                    "Cox proportional hazards model\n",
                    summary$n, "subjects,", summary$nevent, "events",
                    if (len > 0) paste0(" (", len, " missing values removed)"),
                    "\nConcordance: ", summary$concordance[[1]],
                    "\nSE: ", summary$concordance[[2]],
                    "\nR\u00B2: ", summary$rsq[[1]],
                    "\nMax possible: " , summary$rsq[[2]], "\n")

                write(info, file=file)
                suppressWarnings(
                    write.table(tests, file=file, quote=FALSE, sep="\t",
                                append=TRUE))
                write("", file=file, append=TRUE)
                suppressWarnings(
                    write.table(cox, file=file, quote=FALSE, sep="\t",
                                append=TRUE, col.names = NA))
            }
        )

        output$coxTests <- renderDataTable({
            if (is.null(survTerms)) return(NULL)

            pvalue <- signifDigits(tests[, 3])
            tests[, seq(2)] <- roundDigits(tests[ , seq(2), drop=FALSE])
            tests[, 3] <- pvalue
            return(tests)
        }, style="bootstrap", selection='none',
        options=list(info=FALSE, paging=FALSE, searching=FALSE, scrollX=TRUE))

        output$coxGroups <- renderDataTable({
            if (is.null(survTerms)) return(NULL)

            cox <- roundDigits(cox)
            cox[ , "Coefficient"] <- paste(cox[ , "Coefficient"],
                                           cox[ , "Standard error"],
                                           sep = " \u00B1 ")
            cox[ , "Lower 95%"] <- sprintf("%s to %s",
                                           cox[ , "Lower 95%"],
                                           cox[ , "Upper 95%"])
            colnames(cox)[4] <- "95% CI"
            cox <- cox[ , -c(2, 5:6), drop=FALSE]
            return(cox)
        }, style="bootstrap", selection='none', options=list(scrollX=TRUE))
    })

    # Calculate optimal inclusion levels
    output$pvaluePlot <- renderUI({
        subjects      <- getSubjectId()
        psi           <- getInclusionLevels()
        match         <- getClinicalMatchFrom("Inclusion levels")
        splicingEvent <- getEvent()
        # Get user input
        timeStart     <- input$timeStart
        timeStop      <- input$timeStop
        event         <- input$event
        censoring     <- input$censoring
        # Get clinical data for the required attributes
        followup <- "days_to_last_followup"
        clinical <- getClinicalDataForSurvival(timeStart, timeStop, event,
                                               followup)
        samples <- getSelectedGroups(input, "sampleFiltering", "Samples")

        if (is.null(subjects)) {
            hide("psiCutoff")
            return(helpText(icon("exclamation-circle"),
                            "Please load clinical data."))
        } else if (is.null(getInclusionLevels())) {
            hide("psiCutoff")
            return(helpText(icon("exclamation-circle"),
                            "Please load or calculate the quantification of",
                            "alternative splicing events."))
        } else if (is.null(getEvent()) || getEvent() == "") {
            hide("psiCutoff")
            return(helpText(icon("exclamation-circle"),
                            "Please select an alternative splicing event."))
        } else {
            output$survival  <- renderHighchart(NULL)
            output$coxphUI   <- renderUI(NULL)
            # output$coxTests  <- renderDataTable(NULL)
            # output$coxGroups <- renderDataTable(NULL)

            # Assign values to subjects based on their samples
            eventPSI <- assignValuePerSubject(psi[splicingEvent, ], match,
                                              patients=subjects,
                                              samples=unlist(samples))

            show("psiCutoff")
            slider <- uiOutput(ns("cutoffPvalue"))
            label <- tags$label(class="control-label",
                                "-log\u2081\u2080(p-value) plot by cutoff")

            cutoffs <- seq(0, 0.99, 0.01)
            pvaluePlot <- plotSurvivalPvaluesByCutoff(
                clinical=clinical, data=eventPSI, censoring=censoring,
                event=event, timeStart=timeStart, timeStop=timeStop,
                followup=followup, cutoffs=cutoffs)

            # Automatically set minimal p-value
            value <- cutoffs[which.min(unlist(attr(pvaluePlot, "pvalues")))]
            observe({
                if (is.na(value)) value <- 0.5
                updateSliderInput(session, "psiCutoff", value=value)
            })

            if (!is.na(value) && value < 1) {
                return(tagList(slider, label, pvaluePlot))
            } else {
                return(tagList(
                    slider, label, pvaluePlot,
                    div(class="alert alert-warning", "No adequate",
                        "cutoff was found for this splicing event.")))
            }
        }
    })

    # Update contextual information for selected PSI cutoff
    observeEvent(input$psiCutoff, {
        subjects      <- getSubjectId()
        psi           <- getInclusionLevels()
        match         <- getClinicalMatchFrom("Inclusion levels")
        splicingEvent <- getEvent()
        # Get user input
        timeStart     <- input$timeStart
        timeStop      <- input$timeStop
        event         <- input$event
        censoring     <- input$censoring
        psiCutoff     <- input$psiCutoff
        # Get clinical data for the required attributes
        followup <- "days_to_last_followup"
        clinical <- getClinicalDataForSurvival(timeStart, timeStop, event,
                                               followup)
        samples <- getSelectedGroups(input, "sampleFiltering", "Samples")

        if (is.null(splicingEvent) || splicingEvent == "" ||
            is.null(psi) || is.null(subjects)) return(NULL)

        # Assign values to subjects based on their samples
        eventPSI <- assignValuePerSubject(psi[splicingEvent, ], match,
                                          patients=subjects,
                                          samples=unlist(samples))

        pvalue <- testSurvivalCutoff(
            psiCutoff, data=eventPSI, clinical=clinical, censoring=censoring,
            timeStart=timeStart, timeStop=timeStop, event=event,
            session=session, survivalInfo = TRUE)
        surv <- attr(pvalue, "info")

        subjects <- NULL
        if (!is.na(pvalue) && pvalue < 1)
            subjects <- paste0("(", surv$n[1], " vs ", surv$n[2], " subjects)")

        output$cutoffPvalue <- renderUI(
            tagList(div(style="text-align:right; font-size:small",
                        tags$b("p-value of selected cutoff:"), round(pvalue, 3),
                        subjects),
                    tags$br()))
    })

    geneExprSurvSet(session, input, output)
}

attr(survivalUI, "loader") <- "analysis"
attr(survivalUI, "name") <- "Survival analysis"
attr(survivalServer, "loader") <- "analysis"