R/panel_RowDataPlot.R

In iSEE: Interactive SummarizedExperiment Explorer

#' The RowDataPlot panel
#'
#' The RowDataPlot is a panel class for creating a \linkS4class{RowDotPlot} where the y-axis represents a variable from the \code{\link{rowData}} of a \linkS4class{SummarizedExperiment} object.
#' It provides slots and methods for specifying which variable to use on the y-axis (and, optionally, also the x-axis), as well as a method to create the data.frame in preparation for plotting.
#'
#' @section Slot overview:
#' The following slots control the variables to be shown:
#' \itemize{
#' \item \code{YAxis}, a string specifying the row of the \code{\link{rowData}} to show on the y-axis.
#' If \code{NA}, defaults to the first valid field (see \code{?"\link{.refineParameters,RowDotPlot-method}"}).
#' \item \code{XAxis}, string specifying what should be plotting on the x-axis.
#' This can be any one of \code{"None"} or \code{"Row data"}.
#' Defaults to \code{"None"}.
#' \item \code{XAxisRowData}, string specifying the row of the \code{\link{rowData}} to show on the x-axis.
#' If \code{NA}, defaults to the first valid field.
#' }
#'
#' In addition, this class inherits all slots from its parent \linkS4class{RowDotPlot}, \linkS4class{DotPlot} and \linkS4class{Panel} classes.
#'
#' @section Constructor:
#' \code{RowDataPlot(...)} creates an instance of a RowDataPlot class, where any slot and its value can be passed to \code{...} as a named argument.
#'
#' @section Supported methods:
#' In the following code snippets, \code{x} is an instance of a \linkS4class{RowDataPlot} class.
#' Refer to the documentation for each method for more details on the remaining arguments.
#'
#' For setting up data values:
#' \itemize{
#' \item \code{\link{.refineParameters}(x, se)} returns \code{x} after replacing any \code{NA} value in \code{YAxis} or \code{XAxisRowData} with the name of the first valid \code{\link{rowData}} variable.
#' This will also call the equivalent \linkS4class{RowDotPlot} method for further refinements to \code{x}.
#' If no valid row metadata variables are available, \code{NULL} is returned instead.
#' }
#'
#' For defining the interface:
#' \itemize{
#' \item \code{\link{.defineDataInterface}(x, se, select_info)} returns a list of interface elements for manipulating all slots described above.
#' \item \code{\link{.panelColor}(x)} will return the specified default color for this panel class.
#' \item \code{\link{.allowableXAxisChoices}(x, se)} returns a character vector specifying the acceptable variables in \code{\link{rowData}(se)} that can be used as choices for the x-axis. 
#' This consists of all variables with atomic values.
#' \item \code{\link{.allowableYAxisChoices}(x, se)} returns a character vector specifying the acceptable variables in \code{\link{rowData}(se)} that can be used as choices for the y-axis. 
#' This consists of all variables with atomic values.
#' }
#'
#' For monitoring reactive expressions:
#' \itemize{
#' \item \code{\link{.createObservers}(x, se, input, session, pObjects, rObjects)} sets up observers for all slots described above and in the parent classes.
#' This will also call the equivalent \linkS4class{RowDotPlot} method.
#' }
#'
#' For defining the panel name:
#' \itemize{
#' \item \code{\link{.fullName}(x)} will return \code{"Row data plot"}.
#' }
#'
#' For creating the plot:
#' \itemize{
#' \item \code{\link{.generateDotPlotData}(x, envir)} will create a data.frame of row metadata variables in \code{envir}.
#' It will return the commands required to do so as well as a list of labels.
#' }
#'
#' For documentation:
#' \itemize{
#' \item \code{\link{.definePanelTour}(x)} returns an data.frame containing a panel-specific tour.
#' }
#'
#' @section Subclass expectations:
#' Subclasses do not have to provide any methods, as this is a concrete class.
#' 
#' @author Aaron Lun
#'
#' @seealso
#' \linkS4class{RowDotPlot}, for the immediate parent class.
#'
#' @examples
#' #################
#' # For end-users #
#' #################
#'
#' x <- RowDataPlot()
#' x[["XAxis"]]
#' x[["XAxis"]] <- "Row data"
#'
#' ##################
#' # For developers #
#' ##################
#'
#' library(scater)
#' sce <- mockSCE()
#' sce <- logNormCounts(sce)
#'
#' # Spits out a NULL and a warning if is nothing to plot.
#' sce0 <- .cacheCommonInfo(x, sce)
#' .refineParameters(x, sce0)
#'
#' # Replaces the default with something sensible.
#' rowData(sce)$Stuff <- runif(nrow(sce))
#' sce0 <- .cacheCommonInfo(x, sce)
#' .refineParameters(x, sce0)
#'
#' @docType methods
#' @aliases RowDataPlot RowDataPlot-class
#' initialize,RowDataPlot-method
#' .refineParameters,RowDataPlot-method
#' .defineDataInterface,RowDataPlot-method
#' .createObservers,RowDataPlot-method
#' .fullName,RowDataPlot-method
#' .panelColor,RowDataPlot-method
#' .generateDotPlotData,RowDataPlot-method
#' .allowableXAxisChoices,RowDataPlot-method
#' .allowableYAxisChoices,RowDataPlot-method
#' .definePanelTour,RowDataPlot-method
#'
#' @name RowDataPlot-class
NULL

#' @export
RowDataPlot <- function(...) {
    new("RowDataPlot", ...)
}

#' @export
#' @importFrom methods callNextMethod
setMethod("initialize", "RowDataPlot", function(.Object, ...) {
    args <- list(...)
    args <- .emptyDefault(args, .rowDataXAxis, .rowDataXAxisNothingTitle)
    args <- .emptyDefault(args, .rowDataXAxisRowData, NA_character_)
    args <- .emptyDefault(args, .rowDataYAxis, NA_character_)
    do.call(callNextMethod, c(list(.Object), args))
})

.rowDataXAxisNothingTitle <- "None"
.rowDataXAxisRowDataTitle <- "Row data"

#' @export
#' @importFrom methods callNextMethod
setMethod(".refineParameters", "RowDataPlot", function(x, se) {
    x <- callNextMethod()
    if (is.null(x)) {
        return(NULL)
    }

    yaxis <- .allowableYAxisChoices(x, se)
    if (length(yaxis)==0L) {
        warning(sprintf("no valid y-axis 'rowData' fields for '%s'", class(x)[1]))
        return(NULL)
    }

    xaxis <- .allowableXAxisChoices(x, se)
    if (length(xaxis)==0L) {
        warning(sprintf("no valid x-axis 'rowData' fields for '%s'", class(x)[1]))
        return(NULL)
    }

    x <- .replaceMissingWithFirst(x, .rowDataYAxis, yaxis)
    x <- .replaceMissingWithFirst(x, .rowDataXAxisRowData, xaxis)

    x
})

#' @importFrom S4Vectors setValidity2
setValidity2("RowDataPlot", function(object) {
    msg <- character(0)

    msg <- .allowableChoiceError(msg, object, .rowDataXAxis,
        c(.rowDataXAxisNothingTitle, .rowDataXAxisRowDataTitle))

    msg <- .singleStringError(msg, object, c(.rowDataXAxisRowData, .rowDataYAxis))

    if (length(msg)) {
        return(msg)
    }
    TRUE
})

#' @export
#' @importFrom shiny selectInput radioButtons
#' @importFrom methods callNextMethod
setMethod(".defineDataInterface", "RowDataPlot", function(x, se, select_info) {
    panel_name <- .getEncodedName(x)
    .input_FUN <- function(field) { paste0(panel_name, "_", field) }

    list(
        .selectInputHidden(x, .rowDataYAxis,
            label="Column of interest (Y-axis):",
            choices=.allowableYAxisChoices(x, se), 
            selected=x[[.rowDataYAxis]]),
        .radioButtonsHidden(x, .rowDataXAxis, 
            label="X-axis:", inline=TRUE,
            choices=c(.rowDataXAxisNothingTitle, .rowDataXAxisRowDataTitle),
            selected=x[[.rowDataXAxis]]),
        .conditionalOnRadio(.input_FUN(.rowDataXAxis),
            .rowDataXAxisRowDataTitle,
            .selectInputHidden(x, .rowDataXAxisRowData,
                label="Column of interest (X-axis):",
                choices=.allowableXAxisChoices(x, se), 
                selected=x[[.rowDataXAxisRowData]]))
    )
})

#' @export
setMethod(".allowableXAxisChoices", "RowDataPlot", function(x, se) {
    .getCachedCommonInfo(se, "RowDotPlot")$valid.rowData.names
})

#' @export
setMethod(".allowableYAxisChoices", "RowDataPlot", function(x, se) {
    .getCachedCommonInfo(se, "RowDotPlot")$valid.rowData.names
})


#' @export
#' @importFrom shiny updateSelectInput
#' @importFrom methods callNextMethod
setMethod(".createObservers", "RowDataPlot", function(x, se, input, session, pObjects, rObjects) {
    callNextMethod()

    plot_name <- .getEncodedName(x)

    .createProtectedParameterObservers(plot_name,
        fields=c(.rowDataYAxis, .rowDataXAxis, .rowDataXAxisRowData),
        input=input, pObjects=pObjects, rObjects=rObjects)
})

#' @export
setMethod(".fullName", "RowDataPlot", function(x) "Row data plot")

#' @export
setMethod(".panelColor", "RowDataPlot", function(x) "#F2B701")

#' @export
setMethod(".generateDotPlotData", "RowDataPlot", function(x, envir) {
    data_cmds <- list()

    y_lab <- x[[.rowDataYAxis]]

    # NOTE: deparse() automatically adds quotes, AND protects against existing quotes/escapes.
    data_cmds[["y"]] <- sprintf(
        "plot.data <- data.frame(Y=rowData(se)[, %s], row.names=rownames(se));",
        deparse(y_lab)
    )

    # Prepare X-axis data.
    if (x[[.rowDataXAxis]] == .rowDataXAxisNothingTitle) {
        x_lab <- ''
        data_cmds[["x"]] <- "plot.data$X <- factor(character(nrow(se)))"
    } else {
        x_lab <- x[[.rowDataXAxisRowData]]
        data_cmds[["x"]] <- sprintf("plot.data$X <- rowData(se)[, %s];", deparse(x_lab))
    }

    x_title <- ifelse(x_lab == '', x_lab, sprintf("vs %s", x_lab))
    plot_title <- sprintf("%s %s", y_lab, x_title)

    data_cmds <- unlist(data_cmds)
    .textEval(data_cmds, envir)

    list(commands=data_cmds, labels=list(title=plot_title, X=x_lab, Y=y_lab))
})

#' @export
setMethod(".definePanelTour", "RowDataPlot", function(x) {
    collated <- character(0)

    collated <- rbind(
        c(paste0("#", .getEncodedName(x)), sprintf("The <font color=\"%s\">Row data plot</font> panel shows variables from the row metadata (i.e., <code>rowData</code>) of a <code>SummarizedExperiment</code> object or one of its subclasses. Here, each point corresponds to a row (usually a feature) of the <code>SummarizedExperiment</code> object, and the y-axis represents a chosen variable.", .getPanelColor(x))),
        .addTourStep(x, .dataParamBoxOpen, "The <i>Data parameters</i> box shows the available parameters that can be tweaked in this plot.<br/><br/><strong>Action:</strong> click on this box to open up available options."),
        .addTourStep(x, .rowDataYAxis, "We can manually choose the variable to show on the y-axis.", is_selectize=TRUE),
        .addTourStep(x, .rowDataXAxis, "We can also specify what should be shown on the x-axis.<br/><br/><strong>Action:</strong> click on <i>Row data</i> to stratify values by a row metadata field."),
        .addTourStep(x, .rowDataXAxisRowData, "This exposes a new interface element that can be used that can be used to choose a covariate to show on the x-axis.", is_selectize=TRUE)
    )

    rbind(
        data.frame(element=collated[,1], intro=collated[,2], stringsAsFactors=FALSE),
        callNextMethod()
    )
})