R/alluvial.h.R

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

# This file is automatically generated, you probably don't want to edit this

alluvialOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "alluvialOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            vars = NULL,
            condensationvar = NULL,
            excl = FALSE,
            marg = FALSE,
            fill = "first_variable",
            bin = "default",
            orient = "vert",
            usetitle = FALSE,
            mytitle = "Alluvial Plot", ...) {

            super$initialize(
                package="ClinicoPath",
                name="alluvial",
                requiresData=TRUE,
                ...)

            private$..vars <- jmvcore::OptionVariables$new(
                "vars",
                vars)
            private$..condensationvar <- jmvcore::OptionVariable$new(
                "condensationvar",
                condensationvar)
            private$..excl <- jmvcore::OptionBool$new(
                "excl",
                excl,
                default=FALSE)
            private$..marg <- jmvcore::OptionBool$new(
                "marg",
                marg,
                default=FALSE)
            private$..fill <- jmvcore::OptionList$new(
                "fill",
                fill,
                options=list(
                    "first_variable",
                    "last_variable",
                    "all_flows",
                    "values"),
                default="first_variable")
            private$..bin <- jmvcore::OptionList$new(
                "bin",
                bin,
                options=list(
                    "default",
                    "mean",
                    "median",
                    "min_max",
                    "cuts"),
                default="default")
            private$..orient <- jmvcore::OptionList$new(
                "orient",
                orient,
                options=list(
                    "horr",
                    "vert"),
                default="vert")
            private$..usetitle <- jmvcore::OptionBool$new(
                "usetitle",
                usetitle,
                default=FALSE)
            private$..mytitle <- jmvcore::OptionString$new(
                "mytitle",
                mytitle,
                default="Alluvial Plot")

            self$.addOption(private$..vars)
            self$.addOption(private$..condensationvar)
            self$.addOption(private$..excl)
            self$.addOption(private$..marg)
            self$.addOption(private$..fill)
            self$.addOption(private$..bin)
            self$.addOption(private$..orient)
            self$.addOption(private$..usetitle)
            self$.addOption(private$..mytitle)
        }),
    active = list(
        vars = function() private$..vars$value,
        condensationvar = function() private$..condensationvar$value,
        excl = function() private$..excl$value,
        marg = function() private$..marg$value,
        fill = function() private$..fill$value,
        bin = function() private$..bin$value,
        orient = function() private$..orient$value,
        usetitle = function() private$..usetitle$value,
        mytitle = function() private$..mytitle$value),
    private = list(
        ..vars = NA,
        ..condensationvar = NA,
        ..excl = NA,
        ..marg = NA,
        ..fill = NA,
        ..bin = NA,
        ..orient = NA,
        ..usetitle = NA,
        ..mytitle = NA)
)

alluvialResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "alluvialResults",
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        plot = function() private$.items[["plot"]],
        plot2 = function() private$.items[["plot2"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Alluvial Diagrams",
                refs=list(
                    "easyalluvial",
                    "ClinicoPathJamoviModule"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do",
                clearWith=list(
                    "vars")))
            self$add(jmvcore::Image$new(
                options=options,
                title="Alluvial Diagrams",
                name="plot",
                width=600,
                height=450,
                renderFun=".plot",
                requiresData=TRUE,
                clearWith=list(
                    "vars",
                    "excl",
                    "marg",
                    "verb",
                    "fill",
                    "bin",
                    "orient",
                    "usetitle",
                    "mytitle")))
            self$add(jmvcore::Image$new(
                options=options,
                title="`Condensation Plot ${condensationvar}`",
                name="plot2",
                width=600,
                height=450,
                renderFun=".plot2",
                requiresData=TRUE,
                clearWith=list(
                    "vars",
                    "condensationvar"),
                visible="(condensationvar)"))}))

alluvialBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "alluvialBase",
    inherit = jmvcore::Analysis,
    public = list(
        initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
            super$initialize(
                package = "ClinicoPath",
                name = "alluvial",
                version = c(0,0,2),
                options = options,
                results = alluvialResults$new(options=options),
                data = data,
                datasetId = datasetId,
                analysisId = analysisId,
                revision = revision,
                pause = NULL,
                completeWhenFilled = FALSE,
                requiresMissings = FALSE,
                weightsSupport = 'auto')
        }))

#' Alluvial Diagrams
#'
#' 
#' @param data The data as a data frame.
#' @param vars a string naming the variables from \code{data} that contains
#'   the values used for the Alluvial Diagram.
#' @param condensationvar The primary variable to be used for condensation.
#' @param excl Exclude missing values from the analysis.
#' @param marg Include marginal plots.
#' @param fill A list for the argument fill for selecting the variable to be
#'   represented by color. Default is 'first_variable'.
#' @param bin labels for the bins from low to high
#' @param orient Orientation of the plot. Default is 'vertical'.
#' @param usetitle Use a custom title for the plot.
#' @param mytitle Title for the plot.
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#'   \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' @export
alluvial <- function(
    data,
    vars,
    condensationvar,
    excl = FALSE,
    marg = FALSE,
    fill = "first_variable",
    bin = "default",
    orient = "vert",
    usetitle = FALSE,
    mytitle = "Alluvial Plot") {

    if ( ! requireNamespace("jmvcore", quietly=TRUE))
        stop("alluvial requires jmvcore to be installed (restart may be required)")

    if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
    if ( ! missing(condensationvar)) condensationvar <- jmvcore::resolveQuo(jmvcore::enquo(condensationvar))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(vars), vars, NULL),
            `if`( ! missing(condensationvar), condensationvar, NULL))


    options <- alluvialOptions$new(
        vars = vars,
        condensationvar = condensationvar,
        excl = excl,
        marg = marg,
        fill = fill,
        bin = bin,
        orient = orient,
        usetitle = usetitle,
        mytitle = mytitle)

    analysis <- alluvialClass$new(
        options = options,
        data = data)

    analysis$run()

    analysis$results
}