volcanoPlot: Create an interactive volcano plot

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

Create an interactive volcano plot

Description

Convenience function to create volcano plots from results generated within this package. This is mostly used by {sparrow.shiny}.

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_line = c(padj = 0.1),
  xhex = NULL,
  yhex = NULL,
  width = NULL,
  height = NULL,
  shiny_source = "mgvolcano",
  ggtheme = ggplot2::theme_bw(),
  ...
)

Arguments

x	A SparrowResult object, or a data.frame
stats	One of "dge" or resultNames(x)
xaxis, yaxis	the column of the the provided (or extracted) data.frame to use for the xaxis and yaxis of the volcano
idx	The column of the data.frame to use as the identifier for the element in the row. You probably don't want to mess with this
xtfrm	A function that transforms the xaxis column to an appropriate scale for the x-axis. This is the identity function by default, because most often the logFC is plotted as is.
ytfrm	A function that transforms the yaxis column to an appropriate scale for the y-axis. This is the -log10(yval) function by default, because this is how we most often plot the y-axis.
xlab, ylab	x and y axis labels
highlight	A vector of featureIds to highlight, or a GeneSetDb that we can extract the featureIds from for this purpose.
horiz_line	A (optionally named) number vecor (length 1) that indicates where a line should be drawn across the volcano plot. This is usually done to signify statistical significance. When the number is "named", this indicates that you want to find an approximation of the values plotted on y based on some transformation of the values that is the named column of x (like "padj"). The default value c(padj = 0.10) indicates you want to draw a line at approximately where the adjust pvalue of 0.10 is on the y-axis, which is the nominal pvalues.
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.
width, height	the width and height of the output plotly plot
shiny_source	the name of this element that is used in shiny callbacks. Defaults to "mggenes".
ggtheme	a ggplot theme, like the thing returned from ggplot2::theme_bw(), for instance.
...	pass through arguments (not used)

Value

a ploty plot object

Examples

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

lianos/sparrow documentation built on Dec. 8, 2024, 2:19 a.m.