Create an interactive volcano plot — volcanoPlot • multiGSEA

Convenience function to create volcano plots from differents types of objects we generate in this package. This is mostly used by the multiGSEA.shiny package.

volcanoPlot(
  x,
  stats = "dge",
  xaxis = "logFC",
  yaxis = "pval",
  idx,
  xtfrm = base::identity,
  ytfrm = function(vals) -log10(vals),
  xlab = xaxis,
  ylab = sprintf("-log10(%s)", yaxis),
  highlight = NULL,
  horiz_lines = c(padj = 0.1),
  xhex = NULL,
  yhex = NULL,
  width = NULL,
  height = NULL,
  shiny_source = "mgvolcano",
  ggtheme = theme_bw(),
  ...
)

Arguments

highlight	A vector of featureIds to highlight, or a GeneSetDb that we can extract the featureIds from for this purpose.
xhex	The raw `.xv` (not `xtfrm(.xv)`) value that acts as a threshold such that values less than this will be hexbinned.
yhex	the `.yvt` value threshold. Vaues less than this will be hexbinned.

Examples

mg <- exampleMultiGSEAResult()
volcanoPlot(mg)
volcanoPlot(mg, xhex=1, yhex=0.05)