R/jviolin.h.R

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

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

jviolinOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "jviolinOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            dep = NULL,
            group = NULL,
            col = NULL,
            fill = NULL,
            excl = FALSE,
            flip = FALSE,
            themex = "ipsum",
            usexlabel = FALSE,
            xlabel = "",
            useylabel = FALSE,
            ylabel = "", ...) {

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

            private$..dep <- jmvcore::OptionVariable$new(
                "dep",
                dep)
            private$..group <- jmvcore::OptionVariable$new(
                "group",
                group)
            private$..col <- jmvcore::OptionVariable$new(
                "col",
                col)
            private$..fill <- jmvcore::OptionVariable$new(
                "fill",
                fill)
            private$..excl <- jmvcore::OptionBool$new(
                "excl",
                excl,
                default=FALSE)
            private$..flip <- jmvcore::OptionBool$new(
                "flip",
                flip,
                default=FALSE)
            private$..themex <- jmvcore::OptionList$new(
                "themex",
                themex,
                options=list(
                    "ipsum",
                    "grey",
                    "gray",
                    "bw",
                    "linedraw",
                    "light",
                    "dark",
                    "minimal",
                    "classic",
                    "void",
                    "test"),
                default="ipsum")
            private$..usexlabel <- jmvcore::OptionBool$new(
                "usexlabel",
                usexlabel,
                default=FALSE)
            private$..xlabel <- jmvcore::OptionString$new(
                "xlabel",
                xlabel,
                default="")
            private$..useylabel <- jmvcore::OptionBool$new(
                "useylabel",
                useylabel,
                default=FALSE)
            private$..ylabel <- jmvcore::OptionString$new(
                "ylabel",
                ylabel,
                default="")

            self$.addOption(private$..dep)
            self$.addOption(private$..group)
            self$.addOption(private$..col)
            self$.addOption(private$..fill)
            self$.addOption(private$..excl)
            self$.addOption(private$..flip)
            self$.addOption(private$..themex)
            self$.addOption(private$..usexlabel)
            self$.addOption(private$..xlabel)
            self$.addOption(private$..useylabel)
            self$.addOption(private$..ylabel)
        }),
    active = list(
        dep = function() private$..dep$value,
        group = function() private$..group$value,
        col = function() private$..col$value,
        fill = function() private$..fill$value,
        excl = function() private$..excl$value,
        flip = function() private$..flip$value,
        themex = function() private$..themex$value,
        usexlabel = function() private$..usexlabel$value,
        xlabel = function() private$..xlabel$value,
        useylabel = function() private$..useylabel$value,
        ylabel = function() private$..ylabel$value),
    private = list(
        ..dep = NA,
        ..group = NA,
        ..col = NA,
        ..fill = NA,
        ..excl = NA,
        ..flip = NA,
        ..themex = NA,
        ..usexlabel = NA,
        ..xlabel = NA,
        ..useylabel = NA,
        ..ylabel = NA)
)

jviolinResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "jviolinResults",
    inherit = jmvcore::Group,
    active = list(
        todo = function() private$.items[["todo"]],
        plot = function() private$.items[["plot"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Violin Plot",
                refs=list(
                    "ggplot2",
                    "RGraphGallery",
                    "hrbrthemes",
                    "ClinicoPathJamoviModule"))
            self$add(jmvcore::Html$new(
                options=options,
                name="todo",
                title="To Do",
                clearWith=list(
                    "dep",
                    "group")))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot",
                title="`${group} - {dep}`",
                width=600,
                height=450,
                renderFun=".plot",
                requiresData=TRUE,
                clearWith=list(
                    "dep",
                    "group",
                    "col",
                    "fill",
                    "excl",
                    "flip",
                    "themex",
                    "usexlabel",
                    "xlabel",
                    "useylabel",
                    "ylabel")))}))

jviolinBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "jviolinBase",
    inherit = jmvcore::Analysis,
    public = list(
        initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
            super$initialize(
                package = "ClinicoPath",
                name = "jviolin",
                version = c(1,0,0),
                options = options,
                results = jviolinResults$new(options=options),
                data = data,
                datasetId = datasetId,
                analysisId = analysisId,
                revision = revision,
                pause = NULL,
                completeWhenFilled = FALSE,
                requiresMissings = FALSE,
                weightsSupport = 'auto')
        }))

#' Violin Plot
#'
#' 
#' @param data .
#' @param dep .
#' @param group .
#' @param col .
#' @param fill .
#' @param excl .
#' @param flip .
#' @param themex .
#' @param usexlabel .
#' @param xlabel .
#' @param useylabel .
#' @param ylabel .
#' @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
#' }
#'
#' @export
jviolin <- function(
    data,
    dep,
    group,
    col,
    fill,
    excl = FALSE,
    flip = FALSE,
    themex = "ipsum",
    usexlabel = FALSE,
    xlabel = "",
    useylabel = FALSE,
    ylabel = "") {

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

    if ( ! missing(dep)) dep <- jmvcore::resolveQuo(jmvcore::enquo(dep))
    if ( ! missing(group)) group <- jmvcore::resolveQuo(jmvcore::enquo(group))
    if ( ! missing(col)) col <- jmvcore::resolveQuo(jmvcore::enquo(col))
    if ( ! missing(fill)) fill <- jmvcore::resolveQuo(jmvcore::enquo(fill))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(dep), dep, NULL),
            `if`( ! missing(group), group, NULL),
            `if`( ! missing(col), col, NULL),
            `if`( ! missing(fill), fill, NULL))


    options <- jviolinOptions$new(
        dep = dep,
        group = group,
        col = col,
        fill = fill,
        excl = excl,
        flip = flip,
        themex = themex,
        usexlabel = usexlabel,
        xlabel = xlabel,
        useylabel = useylabel,
        ylabel = ylabel)

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

    analysis$run()

    analysis$results
}