plot_volcano {autonomics}R Documentation

Plot volcano

Description

Plot volcano

Usage

plot_volcano(
  object,
  fit = intersect(names(metadata(object)), TESTS)[1],
  contrastdefs = autonomics::contrastdefs(object)[[1]],
  label = feature_name,
  ntop = 1
)

Arguments

object

SummarizedExperiment

fit

'limma', 'lme', 'lm', 'wilcoxon'

contrastdefs

contrastdef vector / matrix / list

label

fvar for labeling top features

ntop

number: n top features to be annotated

Value

ggplot object

Examples

file <- download_data('fukuda20.proteingroups.txt')
object <- read_proteingroups(file, fit='limma', plot=FALSE)
plot_volcano(object)

[Package autonomics version 1.2.0 Index]