volcanoPlot: Create an interactive volcano plot

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

Description

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.

Usage

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)

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.