Proof of concept for creating new panel types in iSEE 2.0

panel_RedDimHexbinPlot.R

setClass("RedDimHexbinPlot", contains="RedDimPlot")

#' The reduced dimension hexbin plot panel
#'
#' Plots reduced dimensions summarizing points into hexagon bins.
#'
#' @section Constructor:
#' \code{RedDimHexbinPlot()} creates an instance of a RedDimHexbinPlot class.
#'
#' @author Kevin Rue
#'
#' @examples
#' #################
#' # For end-users #
#' #################
#'
#' x <- RedDimHexbinPlot()
#' x[["Type"]]
#' x[["Type"]] <- "TSNE"
#'
#' ##################
#' # For developers #
#' ##################
#' 
#'
#' library(scater)
#' sce <- mockSCE()
#' sce <- logNormCounts(sce)
#'
#' # Spits out a NULL and a warning if no reducedDims are available.
#' sce0 <- .cacheCommonInfo(x, sce)
#' .refineParameters(x, sce0)
#'
#' # Replaces the default with something sensible.
#' sce <- runPCA(sce)
#' sce0 <- .cacheCommonInfo(x, sce)
#' .refineParameters(x, sce0)
#'
#' @docType methods
#' @aliases RedDimHexbinPlot RedDimHexbinPlot-class
#' .defineParamInterface,RedDimHexbinPlot-method
#' .createParamObservers,RedDimHexbinPlot-method
#' @name RedDimHexbinPlot
NULL

#' @export
RedDimHexbinPlot <- function() {
    new("RedDimHexbinPlot")
}

#' @export
#' @importFrom methods callNextMethod
setMethod("initialize", "RedDimHexbinPlot", function(.Object, ...) {
    # TODO: Package `hexbin` required for `stat_binhex`
    stopifnot(require(hexbin))
    .Object <- callNextMethod(.Object, ...)
    .Object
})

#' @export
#' @importFrom SingleCellExperiment reducedDimNames reducedDim
#' @importClassesFrom SingleCellExperiment SingleCellExperiment
#' @importFrom methods callNextMethod
setMethod(".cacheCommonInfo", "RedDimHexbinPlot", function(x, se) {
    callNextMethod()
})

#' @export
#' @importFrom SingleCellExperiment reducedDim
#' @importFrom methods callNextMethod
setMethod(".refineParameters", "RedDimHexbinPlot", function(x, se) {
    x <- callNextMethod()
    x
})

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

    if (length(msg)>0) {
        return(msg)
    }
    TRUE
})

#' @export
#' @importFrom SingleCellExperiment reducedDim reducedDimNames
#' @importFrom shiny selectInput
#' @importFrom methods callNextMethod
setMethod(".defineParamInterface", "RedDimHexbinPlot", function(x, se, active_panels) {
    callNextMethod()
})

#' @export
#' @importFrom SingleCellExperiment reducedDim
#' @importFrom shiny observeEvent updateSelectInput
#' @importFrom methods callNextMethod
setMethod(".createParamObservers", "RedDimHexbinPlot", function(x, se, input, session, pObjects, rObjects) {
    callNextMethod()
})

#' @export
setMethod(".getEncodedName", "RedDimHexbinPlot", function(x) "RedDimHexbinPlot")

#' @export
setMethod(".getFullName", "RedDimHexbinPlot", function(x) "Reduced dimension hexbin plot")

#' @export
setMethod(".getCommandsDataXY", "RedDimHexbinPlot", function(x, param_choices) {
    callNextMethod()
})

#' @export
setMethod(".getCommandsPlot", "RedDimHexbinPlot", function(x, param_choices, plot_data, plot_type, labs, is_subsetted, is_downsampled) {
    
    plot_cmds <- list()
    plot_cmds[["ggplot"]] <- "ggplot() +"
    
    # Adding hexbins to the plot.
    new_aes <- .build_aes()
    plot_cmds[["hex"]] <- sprintf("geom_hex(%s, plot.data) +", new_aes)
    plot_cmds[["theme_base"]] <- "theme_bw()"
    
    
    return(unlist(plot_cmds))
})