R/plot.MLP.R

In MLP: MLP

#' Plot the Results of an MLP Run
#' @param x object of class 'MLP'
#' @param y argument added to comply with generic; not used, defaults to NULL
#' @param type character of length one; one of 'barplot', 'GOgraph' or 'quantileCurves'
#' @param ... further arguments for the plot functions for each type 
#' @return for type = "barplot", the midpoints of the barplot 
#' @S3method plot MLP
#' @method plot MLP
#' @examples pathExampleMLPResult <- system.file("exampleFiles", "exampleMLPResult.rda", package = "MLP")
#' load(pathExampleMLPResult)
#' dev.new(width = 10, height = 10)
#' op <- par(mar = c(30, 10, 6, 2))
#' plot(exampleMLPResult, type = "barplot")
#' par(op)
#' plot(exampleMLPResult, type = "quantileCurves")
#' if (require(GO.db) && require(Rgraphviz)){
#'   plot(exampleMLPResult, type = "GOgraph")
#' }
#' @export
plot.MLP <- function(x, y = NULL, type = c("barplot", "GOgraph", "quantileCurves") , ...){
  type <- match.arg(type)
  switch(type, 
      barplot = {
        mlpBarplot(object = x, ...)
      }, GOgraph = {
        plotGOgraph(object = x, ...)
      }, quantileCurves = {
        if (is.null(attr(x, "quantileCurveInformation"))){
          stop("A quantile curve plot can only be drawn for an MLP run for which smoothPValues = TRUE")
        } else {
           quantileCurveInformation <- attr(x, "quantileCurveInformation")
           plotQuantileCurves(x0 = quantileCurveInformation$x0, 
               y0 = quantileCurveInformation$y0,
               hqi = quantileCurveInformation$hqi, 
               xtp = quantileCurveInformation$xtp,
               qi = quantileCurveInformation$qi, 
               lqi = quantileCurveInformation$lqi,
               ...) # dots a.o. for sym argument
        }
      }) 
}