posplot: Positives plot
In plger/RNAontheBENCH: RNAontheBENCH - Benchmark of RNAseq quantification and DEA

Produces a 'positives plot', i.e. a plot analogous to the ROC curve, showing the positives across conditions against the positives within condition, across a significance thresholds.

posplot(p, fp1, fp2 = NULL, subsamp = 200, pround = 2, add = FALSE,
  xlab = "DEGs between replicates", ylab = "DEGs between conditions",
  main = "Positives plot", col = "black", xlim = NULL, ylim = NULL,
  lwd = 3, lty = 1, use.fdr = FALSE, auc.plotted = FALSE,
  ncores = NULL)

`p`	A vector of p-values across conditions.
`fp1`	A vector of p-values within condition A.
`fp2`	An optional vector of p-values within condition B.
`subsamp`	The maximum number of datapoints to plot. Default 200.
`pround`	Rounding of the log10 p-values (default 2 digits). Increasing this will increase the precision of the curve, at a speed in cost.
`add`	Whether to add the data series on top of the current graph. Default FALSE (produces a new plot).
`xlab`	Passed to the plot function.
`ylab`	Passed to the plot function.
`main`	Passed to the plot function.
`col`	Passed to the plot function, default black.
`xlim`	Passed to the plot function.
`ylim`	Passed to the plot function.
`lwd`	Passed to the plot function, default 3.
`lty`	Passed to the plot function, default 1.
`use.fdr`	Logical; whether to use adjust the p-values for multiple testing (FDR); default FALSE.
`auc.plotted`	Whether to compute the area under the plotted curve (i.e. within plotting limits) instead of that of the full curve (default FALSE).
`ncores`	Number of threads used for computing (default detectedCores()-1)