enrichment_barplot: Create a barplot using ggplot2 to show enrichment results

In ycl6/topGO-feat: Enrichment Analysis for Gene Ontology

Description

This function takes a topGOdata object and a topGOresult object to display the enrichment statistics of top N GO terms. It wraps ggplot2 plotting, and returns a ggplot2 graphic object.

Usage

enrichment_barplot(object, result, showTerms = 10, numChar = 40, 
		   orderBy = "Scores", y = "Count", 
		   xlab = NULL, ylab = NULL, title = NULL)

Arguments

object	(Required). A topGOdata object.
result	(Required). A topGOresult object.
showTerms	(Optional). A single integer or a character vector of GO ID. Default is 10. Indicates the number of GO terms to show.
numChar	(Optional). A single integer. Default is 40. Indicates the number characters to keep in the GO term description
orderBy	(Optional). A character string. Default is "Scores". Indicates how to order the test results before subsetting to taking top N terms. It can be either "Scores" (i.e. p-values) or "Ratio"
y	(Optional). A character string. Default is "Count". Indicates the variable that should be mapped to the y-axis. It can be either "Count" or "Ratio"
xlab	(Optional). A character string. Default is NULL. Indicates the x-axis label.
ylab	(Optional). A character string. Default is NULL. Indicates the y-axis label.
title	(Optional). A character string. Default is NULL Indicates the main title for the graphic.

Value

A ggplot2 plot object

See Also

ggplot

Examples

data(GOdata)
data(results.tGO)

resultFisher <- runTest(GOdata, algorithm = "classic", statistic = "fisher")
enrichment_barplot(GOdata, resultFisher, showTerms = 10, numChar = 40,
                   orderBy = "Scores", y = "Count")

ycl6/topGO-feat documentation built on Aug. 12, 2020, 12:55 a.m.