enrichMAplot: MA plot of enriched annotations.

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Make an MA-like plot of enriched annotations, similar to the commonly used plots in differential expression analysis.

Usage

enrichMAplot(x, pvalue = "pvals", siglev = 0.05, size = 1,
  alpha = 1)

## S4 method for signature 'list'
enrichMAplot(x, pvalue = "pvals", siglev = 0.05,
  size = 1, alpha = 1)

## S4 method for signature 'AnnotatedDataFrame'
enrichMAplot(x, pvalue = "pvals",
  siglev = 0.05, size = 1, alpha = 1)

Arguments

x	AnnotatedDataFrame object, or a list of those.
pvalue	Character, one of c("pvals", "padj").
siglev	Numeric, significance level to be used for plotting.
size	Numeric, size of points in plot.
alpha	Numeric, between 0 and 1, indicating points' transparency.

Value

A ggplot object.

Examples

require(ggplot2)

HD59_KO
enrichMAplot(HD59_KO)
enrichMAplot(HD59_KO, pvalue = "padj")
enrichMAplot(HD59_KO, siglev = 0.01)
enrichMAplot(HD59_KO, pvalue = "padj", siglev = 0.01)

x <- list(disease = LD94_KO, healthy = HD59_KO)
enrichMAplot(x)

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.