vol3d: Make a 3D volcano plot combine 2 results objects into one...

In kevincjnixon/BinfTools: Useful functions for standard analyses

Make a 3D volcano plot combine 2 results objects into one volcano plot - note this is experimental and not usually done

Description

Make a 3D volcano plot combine 2 results objects into one volcano plot - note this is experimental and not usually done

Usage

vol3d(
  x,
  y,
  xlab = "res1",
  ylab = "res2",
  pval = 0.05,
  pcol = "pvalue",
  usep = NULL
)

Arguments

x	DESeq2 results object to be plotted for the x-axis
y	DESeq2 results object to be plotted for the y-axis
xlab	Contrast name for x. Default='res1'.
ylab	Contrast name for y. Default='res2'.
pval	significance threshold for differential genes. Default is 0.05
pcol	Character of either 'pvalue' or 'padj' indicating which column to use to plot significance. Default is "pvalue".
usep	numeric of either 1 or 2 indicating which p-values to plot (x or y, respectively). If left NULL (default). P-values from both x and y are combined using Fisher's combined probability test, and the resulting p-values are plotted.

Value

3D volcano plot with every combination of up/down-regulated genes labeled and a data frame of the combined data used to generate the plot.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.