barplot: Barplot for methylGSA analysis result

In methylGSA: Gene Set Analysis Using the Outcome of Differential Methylation

Description

This function visualizes methylGSA analysis result by barplot.

Usage

barplot(res, xaxis = "Size", num = 5, colorby = "padj", title = "")

Arguments

res	A data frame which contains methylGSA analysis result.
xaxis	A string which specify the x-axis in the barplot. Either "Size" (number of genes in gene set) or "Count" (number of significant genes in gene set). Default is "Size". "Count" option is not available for methylglm and methylRRA(GSEA) result.
num	An integer. Number of gene sets to display on the barplot. Default is 5.
colorby	A string. Either "pvalue" or "padj". Default is "padj".
title	A string. Barplot title. Default is NULL.

Details

The implementation of the function is adapted from barplot function in enrichplot package.

Value

ggplot object

References

Yu G (2018). enrichplot: Visualization of Functional Enrichment Result. R package version 1.0.2, https://github.com/GuangchuangYu/enrichplot.

Examples

res = data.frame(ID = c("04144", "04510", "04740", "04810", "05200"),
                 Description = c("Endocytosis", "Focal adhesion", 
                 "Olfactory transduction", 
                 "Regulation of actin cytoskeleton", "Pathways in cancer"),
                 Size = c(201, 200, 388, 213, 326),
                 pvalue = c(0.481, 0.696, 1, 1, 1),
                 padj = 1
                 )
barplot(res)

methylGSA documentation built on Nov. 8, 2020, 8:29 p.m.