grandR (version 0.2.5)

MAPlot: Make an MA plot

Description

Plot average expression vs. log2 fold changes

Usage

MAPlot(
  data,
  analysis = Analyses(data)[1],
  aest = aes(),
  p.cutoff = 0.05,
  lfc.cutoff = 1,
  label.numbers = TRUE,
  highlight = NULL,
  label = NULL,
  label.repel = 1
)

Value

a ggplot object

Arguments

data

the grandR object that contains the data to be plotted

analysis

the analysis to plot (default: first analysis)

aest

parameter to set visual attributes of the plot

p.cutoff

p-value cutoff (default: 0.05)

lfc.cutoff

log fold change cutoff (default: 1)

label.numbers

if TRUE, label the number of genes

highlight

highlight these genes; can be either numeric indices, gene names, gene symbols or a logical vector (see details)

label

label these genes; can be either numeric indices, gene names, gene symbols or a logical vector (see details)

label.repel

force to repel labels from points and each other (increase if labels overlap)