R/plotMarginals.R

In consensus: Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

plotMarginals <- function (consfit, param = c("average", "sensitivity", "precision"), 
          pal = palette(), xlim = NULL, ...) 
{
  stopifnot(is(consfit, "ConsensusFit"))
  param <- match.arg(param)
  if (length(pal) < ncol(consfit@a_i)) {
    stop("Palette size must be at least the number of platforms/conditions")
  }
  toplot <- switch(param, average = {
    consfit@a_i
  }, sensitivity = {
    consfit@b_i
  }, precision = {
    log(consfit@d_i)
  })
  
  if (is.null(xlim)) {
    xlim = range(toplot)
  } else {
    toplot <- toplot[apply(toplot, 1, function (x) all(x>=xlim[1] & x<=xlim[2])),]
  }
  densities <- apply(toplot, 2, density)
  maxdens <- max(unlist(lapply(densities, function(x) max(x$y))))
  plabel <- switch(param, average = {
    "a_i"
  }, sensitivity = {
    "b_i"
  }, precision = "Log (d_i)")
  plot(1, 1, xlim = xlim, ylim = c(-(maxdens/10), maxdens), 
       type = "n", xlab = plabel, ylab = "Density", main = paste0("Marginals: ", 
                                                                  param))
  for (i in seq_len(ncol(toplot))) {
    lines(densities[[i]], lwd = 2, col = pal[i])
  }
  abline(h = 0, col = "gray")
  legend(min(toplot), 0, colnames(toplot), text.col = pal, 
         horiz = TRUE, bty = "n", ...)
}