volcano.plot: Volcano plot

In fchen365/surf: Statistical Utility for RBP (RNA binding protein) Functions

Description

Create a volcano plot for the DrSeq results, stratified by alternative transcriptional regulation (ATR) event types. A volcano plot is a scatter plot of tested units, where log2 fold change is in x-axis, and -log10(p.value) is in y-axis.

Usage

volcano.plot(object, ...)

## S4 method for signature 'drseqResults'
volcano.plot(
  object,
  lfc.cutoff = c(-1, 1),
  fdr.cutoff = 0.01,
  x.limits = c(-15, 15),
  y.limits = c(0, 50),
  remove.portion.grey = 0,
  remove.portion.color = 0,
  colrs = setNames(surf.colors, surf.events)
)

## S4 method for signature 'surf'
volcano.plot(object, ...)

Arguments

object	a drseqResults object.
...	various parameters.
lfc.cutoff	numeric(2), the range of log2 fold change that is consider NOT significant.
fdr.cutoff	numeric(1), significance level of adjusted p-value.
x.limits	numeric(2), range of log2 fold change. Any values beyond this range will be projected onto the boundary.
y.limits	numeric(2), range of -log10(p.value). Any values beyond this range will be projected onto the boundary.
remove.portion.grey	numeric, between 0 and 1, the portion of non-significant points to be randomly remove. This is only for speeding up plotting.
remove.portion.color	numeric, between 0 and 1, the portion of significant points to be randomly remove. This is only for speeding up plotting.
colrs	a character vector, named by ATR event types, whose values are the corresponding color codes.

Details

By default, ATR type are colored with the Paired palette.

Value

a ggplot object.

fchen365/surf documentation built on June 18, 2021, 12:02 p.m.