R/tidyplots.h.R

In sbalci/ClinicoPathJamoviModule: Analysis for Clinicopathological Research

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

tidyplotsOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "tidyplotsOptions",
    inherit = jmvcore::Options,
    public = list(
        initialize = function(
            xvar = NULL,
            yvar = NULL,
            color = NULL,
            plotType = "points",
            pointType = "basic",
            showMean = FALSE,
            showSEM = FALSE,
            showCI = FALSE,
            colorScheme = "friendly",
            plotTitle = "",
            xLabel = "",
            yLabel = "", ...) {

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

            private$..xvar <- jmvcore::OptionVariable$new(
                "xvar",
                xvar)
            private$..yvar <- jmvcore::OptionVariable$new(
                "yvar",
                yvar)
            private$..color <- jmvcore::OptionVariable$new(
                "color",
                color)
            private$..plotType <- jmvcore::OptionList$new(
                "plotType",
                plotType,
                options=list(
                    "points",
                    "line",
                    "bar",
                    "boxplot"),
                default="points")
            private$..pointType <- jmvcore::OptionList$new(
                "pointType",
                pointType,
                options=list(
                    "basic",
                    "beeswarm",
                    "jitter"),
                default="basic")
            private$..showMean <- jmvcore::OptionBool$new(
                "showMean",
                showMean,
                default=FALSE)
            private$..showSEM <- jmvcore::OptionBool$new(
                "showSEM",
                showSEM,
                default=FALSE)
            private$..showCI <- jmvcore::OptionBool$new(
                "showCI",
                showCI,
                default=FALSE)
            private$..colorScheme <- jmvcore::OptionList$new(
                "colorScheme",
                colorScheme,
                options=list(
                    "friendly",
                    "viridis",
                    "seaside"),
                default="friendly")
            private$..plotTitle <- jmvcore::OptionString$new(
                "plotTitle",
                plotTitle,
                default="")
            private$..xLabel <- jmvcore::OptionString$new(
                "xLabel",
                xLabel,
                default="")
            private$..yLabel <- jmvcore::OptionString$new(
                "yLabel",
                yLabel,
                default="")

            self$.addOption(private$..xvar)
            self$.addOption(private$..yvar)
            self$.addOption(private$..color)
            self$.addOption(private$..plotType)
            self$.addOption(private$..pointType)
            self$.addOption(private$..showMean)
            self$.addOption(private$..showSEM)
            self$.addOption(private$..showCI)
            self$.addOption(private$..colorScheme)
            self$.addOption(private$..plotTitle)
            self$.addOption(private$..xLabel)
            self$.addOption(private$..yLabel)
        }),
    active = list(
        xvar = function() private$..xvar$value,
        yvar = function() private$..yvar$value,
        color = function() private$..color$value,
        plotType = function() private$..plotType$value,
        pointType = function() private$..pointType$value,
        showMean = function() private$..showMean$value,
        showSEM = function() private$..showSEM$value,
        showCI = function() private$..showCI$value,
        colorScheme = function() private$..colorScheme$value,
        plotTitle = function() private$..plotTitle$value,
        xLabel = function() private$..xLabel$value,
        yLabel = function() private$..yLabel$value),
    private = list(
        ..xvar = NA,
        ..yvar = NA,
        ..color = NA,
        ..plotType = NA,
        ..pointType = NA,
        ..showMean = NA,
        ..showSEM = NA,
        ..showCI = NA,
        ..colorScheme = NA,
        ..plotTitle = NA,
        ..xLabel = NA,
        ..yLabel = NA)
)

tidyplotsResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
    "tidyplotsResults",
    inherit = jmvcore::Group,
    active = list(
        instructions = function() private$.items[["instructions"]],
        plot = function() private$.items[["plot"]]),
    private = list(),
    public=list(
        initialize=function(options) {
            super$initialize(
                options=options,
                name="",
                title="Tidy Plots",
                refs=list(
                    "tidyplots",
                    "ggplot2",
                    "dplyr",
                    "rlang",
                    "jmvcore",
                    "R6"))
            self$add(jmvcore::Html$new(
                options=options,
                name="instructions",
                title="Instructions",
                visible="(xvar === null || yvar === null)"))
            self$add(jmvcore::Image$new(
                options=options,
                name="plot",
                title="Plot",
                renderFun=".plot",
                requiresData=TRUE,
                width=600,
                height=400,
                clearWith=list(
                    "xvar",
                    "yvar",
                    "color",
                    "plotType",
                    "pointType",
                    "showMean",
                    "showSEM",
                    "showCI",
                    "colorScheme",
                    "plotTitle",
                    "xLabel",
                    "yLabel")))}))

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

#' Tidy Plots
#'
#' 
#' @param data The data as a data frame.
#' @param xvar .
#' @param yvar .
#' @param color .
#' @param plotType .
#' @param pointType .
#' @param showMean .
#' @param showSEM .
#' @param showCI .
#' @param colorScheme .
#' @param plotTitle .
#' @param xLabel .
#' @param yLabel .
#' @return A results object containing:
#' \tabular{llllll}{
#'   \code{results$instructions} \tab \tab \tab \tab \tab a html \cr
#'   \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' @export
tidyplots <- function(
    data,
    xvar,
    yvar,
    color,
    plotType = "points",
    pointType = "basic",
    showMean = FALSE,
    showSEM = FALSE,
    showCI = FALSE,
    colorScheme = "friendly",
    plotTitle = "",
    xLabel = "",
    yLabel = "") {

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

    if ( ! missing(xvar)) xvar <- jmvcore::resolveQuo(jmvcore::enquo(xvar))
    if ( ! missing(yvar)) yvar <- jmvcore::resolveQuo(jmvcore::enquo(yvar))
    if ( ! missing(color)) color <- jmvcore::resolveQuo(jmvcore::enquo(color))
    if (missing(data))
        data <- jmvcore::marshalData(
            parent.frame(),
            `if`( ! missing(xvar), xvar, NULL),
            `if`( ! missing(yvar), yvar, NULL),
            `if`( ! missing(color), color, NULL))


    options <- tidyplotsOptions$new(
        xvar = xvar,
        yvar = yvar,
        color = color,
        plotType = plotType,
        pointType = pointType,
        showMean = showMean,
        showSEM = showSEM,
        showCI = showCI,
        colorScheme = colorScheme,
        plotTitle = plotTitle,
        xLabel = xLabel,
        yLabel = yLabel)

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

    analysis$run()

    analysis$results
}