barplot: barplot for fet enrichment test

In zhuchcn/HTSet: High through-put experiment dataset container

Description

This function makes bar plot for top most positively and negatively enriched levels.

Usage

barplot(x, ...)

## S3 method for class 'EnrichmentFET'
barplot(
  x,
  num = 6,
  greater = 3,
  less = 3,
  text.size = 10,
  fill = "gray20",
  panel.ratio = 1.2,
  title,
  ...
)

Arguments

x	EnrichmentFET. Returned by enrichment_test with test equals to fet.
...	other params not supported
num	integer. Number of categories to display. Use it when alternative equals to greater, less, or two.sided.
greater	integer. Number of categories which are greater. Use it when alternative equals to both.
less	integer. Number of categories which are less. Use it when alternative equals to both.
text.size	integer
fill	character. Bar fill color
panel.ratio	numeric. The ratio of left and right panels.
title	character. The title of the plot.

Value

a ggplot object

Author(s)

Chenghao Zhu

See Also

enrichment_test

Examples

lpd = transform_by_sample(lipidome, function(x) log(x/sum(x)))
design = model.matrix(~Treatment * Timepoint + Subject, data = lpd$pdata)
fit = model_fit(lpd, design, "TreatmentMed:TimepointPre", "limma")
en = enrichment_test(lpd, fit, "class", "fet")
barplot(en)
en = enrichment_test(lpd, fit, "class", "fet", alternative = "greater")
barplot(en)

zhuchcn/HTSet documentation built on April 10, 2020, 4:51 p.m.